Insecticidal combinations of pip-72 and methods of use

ABSTRACT

Compositions and methods for controlling pests are provided. The methods involve transforming organisms with one or more nucleic acid sequence encoding insecticidal protein(s) and one or more silencing element(s). In particular, the nucleic acid sequences are useful for preparing plants and microorganisms that possess insecticidal activity. Thus, transformed bacteria, plants, plant cells, plant tissues and seeds are provided. Compositions are insecticidal nucleic acids and proteins of bacterial species. The sequences find use in the construction of expression vectors for subsequent transformation into organisms of interest including plants, as probes for the isolation of other homologous (or partially homologous) genes. The molecular and breeding stacks find use in controlling, inhibiting growth or killing Lepidopteran, Coleopteran, Dipteran, fungal, Hemipteran and nematode pest populations and for producing compositions with insecticidal activity.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims priority to U.S. Provisional Application No.62/131,564, filed Mar. 11, 2015 and U.S. Provisional Application No.62/287,272, filed Jan. 26, 2016, which is hereby incorporated herein inits entirety by reference.

REFERENCE TO SEQUENCE LISTING SUBMITTED ELECTRONICALLY

A sequence listing having the file name “6578_sequence_listing.txt”created on Jan. 26, 2016, and having a size of 587 kilobytes is filed incomputer readable form concurrently with the specification. The sequencelisting is part of the specification and is herein incorporated byreference in its entirety.

FIELD

This disclosure relates to the field of molecular biology. Provided arestacks of PIP-72 polypeptide genes that encode pesticidal proteins andsilencing elements. These pesticidal proteins, the RNAi traits, and thenucleic acid sequences that encode them are useful in preparingpesticidal formulations and in the production of transgenicpest-resistant plants.

BACKGROUND

Biological control of insect pests of agricultural significance using amicrobial agent, such as fungi, bacteria or another species of insectaffords an environmentally friendly and commercially attractivealternative to synthetic chemical pesticides. Generally speaking, theuse of biopesticides presents a lower risk of pollution andenvironmental hazards and biopesticides provide greater targetspecificity than is characteristic of traditional broad-spectrumchemical insecticides. In addition, biopesticides often cost less toproduce and thus improve economic yield for a wide variety of crops.

Certain species of microorganisms of the genus Bacillus are known topossess pesticidal activity against a range of insect pests includingLepidoptera, Diptera, Coleoptera, Hemiptera and others. Bacillusthuringiensis (Bt) and Bacillus popilliae are among the most successfulbiocontrol agents discovered to date. Insect pathogenicity has also beenattributed to strains of B. larvae, B. lentimorbus, B. sphaericus and B.cereus. Microbial insecticides, particularly those obtained fromBacillus strains, have played an important role in agriculture asalternatives to chemical pest control.

Crop plants have been developed with enhanced insect resistance bygenetically engineering crop plants to produce pesticidal proteins fromBacillus. For example, corn and cotton plants have been geneticallyengineered to produce pesticidal proteins isolated from strains of Bt.These genetically engineered crops are now widely used in agricultureand have provided the farmer with an environmentally friendlyalternative to traditional insect-control methods. While they haveproven to be very successful commercially, these genetically engineered,insect-resistant crop plants provide resistance to only a narrow rangeof the economically important insect pests. In some cases, insects candevelop resistance to different insecticidal compounds, which raises theneed to identify alternative biological control agents for pest control.

Accordingly, there remains a need for new pesticidal proteins withdifferent ranges of insecticidal activity against insect pests, e.g.,insecticidal proteins which are active against a variety of insects inthe order Lepidoptera and the order Coleoptera including but not limitedto insect pests that have developed resistance to existing insecticides.

SUMMARY

Compositions and methods for conferring pesticidal activity to bacteria,plants, plant cells, tissues and seeds are provided. Compositionsinclude nucleic acid molecules encoding sequences for pesticidal andinsecticidal PIP-72 polypeptides and polynucleotides encoding RNAisilencing elements, vectors comprising those nucleic acid molecules, andhost cells comprising the vectors. The nucleic acid sequences can beused in DNA constructs or expression cassettes for transformation andexpression in organisms, including microorganisms and plants. Thenucleotide or amino acid sequences may be synthetic sequences that havebeen designed for expression in an organism including, but not limitedto, a microorganism or a plant. Compositions also comprise transformedbacteria, plants, plant cells, tissues and seeds.

In particular, isolated or recombinant nucleic acid molecules areprovided encoding Pseudomonas Insecticidal Protein-72 (PIP-72)polypeptides. Additionally, amino acid sequences corresponding to thePIP-72 polypeptides are encompassed. Provided are isolated orrecombinant nucleic acid molecules capable of encoding a PIP-72polypeptide of SEQ ID NO: 849. Nucleic acid sequences that arecomplementary to a nucleic acid sequence of the embodiments or thathybridize to a sequence of the embodiments are also encompassed. Alsoprovided are isolated or recombinant PIP-72 polypeptides of SEQ ID NO:849.

Methods are provided for producing the PIP-72 polypeptides and silencingelements, and for using those polypeptides and silencing elements forcontrolling or killing a Lepidopteran, Coleopteran, nematode, fungi,and/or Dipteran pests. The transgenic plants of the embodiments expressone or more of the PIP-72 polypeptides and one or more silencingelements. In various embodiments, the transgenic plant further comprisesone or more additional genes for insect resistance, for example, one ormore additional genes for controlling Coleopteran, Lepidopteran,Hemipteran or nematode pests. The transgenic plant may further compriseany gene imparting an agronomic trait of interest.

Silencing target polynucleotides or active variants and fragmentsthereof of US Patent Application Publication No. US2014/0275208 andUS2015/0257389 are provided. Silencing elements designed in view ofthese target polynucleotides of US Patent Application Publication No.US2014/0275208 and US2015/0257389 are provided which, when ingested bythe pest, decrease the expression of one or more of the target sequencesand thereby controls the pest (i.e., has insecticidal activity). In oneembodiment of the invention, one or more nucleic acid molecules encodingPIP-72 polypeptides are provided in a molecular stack or expressioncassette with one or more silencing targets or silencing elements setforth in US Patent Application Publication Number US2014/0275208 orUS2015/0257389.

The compositions and methods of the embodiments are useful for theproduction of organisms with enhanced pest resistance or tolerance.These organisms and compositions comprising the organisms are desirablefor agricultural purposes.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 shows a graph representing the nodal injury score of western cornrootworm feeding on T0 plants expressing either a stacked constructcomprising a polynucleotide encoding a PIP-72 polypeptide and RyanRsilencing element (SEQ ID NO: 993) or negative control line, HC69.

FIG. 2 shows a graph representing T0 plant expression of RyanR silencingelement either as a stacked construct comprising a polynucleotideencoding a PIP-72 polypeptide and RyanR silencing element (SEQ ID NO:993) or negative control line, HC69.

FIG. 3 shows a graph representing T0 plant expression of PIP-72 eitheras a stacked construct comprising a polynucleotide encoding a PIP-72polypeptide and RyanR silencing element (SEQ ID NO: 993) or negativecontrol line, HC69.

DETAILED DESCRIPTION

It is to be understood that this disclosure is not limited to theparticular methodology, protocols, cell lines, genera, and reagentsdescribed, as such may vary. It is also to be understood that theterminology used herein is for the purpose of describing particularembodiments only, and is not intended to limit the scope of the presentdisclosure.

As used herein the singular forms “a”, “and”, and “the” include pluralreferents unless the context clearly dictates otherwise. Thus, forexample, reference to “a cell” includes a plurality of such cells andreference to “the protein” includes reference to one or more proteinsand equivalents thereof known to those skilled in the art, and so forth.All technical and scientific terms used herein have the same meaning ascommonly understood to one of ordinary skill in the art to which thisdisclosure belongs unless clearly indicated otherwise.

The present disclosure is drawn to compositions and methods forcontrolling pests. The methods involve transforming organisms withnucleic acid sequences encoding a PIP-72 polypeptide and a silencingelement or other pesticidal agent as disclosed herein. In particular,the nucleic acid sequences of the embodiments are useful for preparingplants and microorganisms that possess pesticidal activity. Thus,transformed bacteria, plants, plant cells, plant tissues and seeds areprovided. The compositions are pesticidal nucleic acids and proteins ofbacterial species. The nucleic acid sequences find use in theconstruction of expression vectors for subsequent transformation intoorganisms of interest. The PIP-72 polypeptides find use in controllingor killing Lepidopteran, Coleopteran, Dipteran, fungal, Hemipteran andnematode pest populations and for producing compositions with pesticidalactivity. Insect pests of interest include, but are not limited to,Lepidoptera species including but not limited to: diamond-back moth,e.g., Helicoverpa zea Boddie; soybean looper, e.g., Pseudoplusiaincludens Walker; and velvet bean caterpillar e.g., Anticarsiagemmatalis Hübner and Coleoptera species including but not limited toWestern corn rootworm (Diabrotica virgifera)—WCRW, Southern cornrootworm (Diabrotica undecimpunctata howardi)—SCRW, and Northern cornrootworm (Diabrotica barber')—NCRW.

“Pesticidal protein” is used herein to refer to a toxin that has toxicactivity against one or more pests, including, but not limited to,members of the Lepidoptera, Diptera, Hemiptera and Coleoptera orders orthe Nematoda phylum or a protein that has homology to such a protein.Pesticidal proteins have been isolated from organisms including, forexample, Bacillus sp., Pseudomonas sp., Photorhabdus sp., Xenorhabdussp., Clostridium bifermentans and Paenibacillus popilliae. Pesticidalproteins include but are not limited to: insecticidal proteins fromPseudomonas sp. such as PSEEN3174 (Monalysin; (2011) PLoS Pathogens7:1-13); from Pseudomonas protegens strain CHAO and Pf-5 (previouslyfluorescens) (Pechy-Tarr, (2008) Environmental Microbiology10:2368-2386; GenBank Accession No. EU400157); from PseudomonasTaiwanensis (Liu, et al., (2010) J. Agric. Food Chem., 58:12343-12349)and from Pseudomonas pseudoalcligenes (Zhang, et al., (2009) Annals ofMicrobiology 59:45-50 and Li, et al., (2007) Plant Cell Tiss. OrganCult. 89:159-168); insecticidal proteins from Photorhabdus sp. andXenorhabdus sp. (Hinchliffe, et al., (2010) The Open Toxicology Journal,3:101-118 and Morgan, et al., (2001) Applied and Envir. Micro.67:2062-2069); U.S. Pat. No. 6,048,838, and U.S. Pat. No. 6,379,946; aPIP-1 polypeptide of U.S. Ser. No. 13/792,861; an AfIP-1A and/or AfIP-1Bpolypeptides of U.S. Ser. No. 13/800,233; a PHI-4 polypeptides of U.S.Ser. No. 13/839,702; PIP-47 polypeptides of U.S. Ser. No. 61/866,747;the insecticidal proteins of U.S. Ser. No. 61/863,761 and 61/863,763;and δ-endotoxins including but not limited to: the Cry1, Cry2, Cry3,Cry4, Cry5, Cry6, Cry7, Cry8, Cry9, Cry10, Cry11, Cry12, Cry13, Cry14,Cry15, Cry16, Cry17, Cry18, Cry19, Cry20, Cry21, Cry22, Cry23, Cry24,Cry25, Cry26, Cry27, Cry 28, Cry 29, Cry 30, Cry31, Cry32, Cry33, Cry34,Cry35,Cry36, Cry37, Cry38, Cry39, Cry40, Cry41, Cry42, Cry43, Cry44,Cry45, Cry 46, Cry47, Cry49, Cry 51, Cry52, Cry 53, Cry 54, Cry55,Cry56, Cry57, Cry58, Cry59. Cry60, Cry61, Cry62, Cry63, Cry64, Cry65,Cry66, Cry67, Cry68, Cry69, Cry70 and Cry71 classes of δ-endotoxin genesand the B. thuringiensis cytolytic cyt1 and cyt2 genes. Members of theseclasses of B. thuringiensis insecticidal proteins include, but are notlimited to Cry1Aa1 (Accession #AAA22353); Cry1Aa2 (Accession #Accession#AAA22552); Cry1Aa3 (Accession #BAA00257); Cry1Aa4 (Accession#CAA31886); Cry1Aa5 (Accession #BAA04468); Cry1Aa6 (Accession#AAA86265); Cry1Aa7 (Accession #AAD46139); Cry1Aa8 (Accession #I26149);Cry1Aa9 (Accession #BAA77213); Cry1Aa10 (Accession #AAD55382); Cry1Aa11(Accession #CAA70856); Cry1Aa12 (Accession #AAP80146); Cry1Aa13(Accession #AAM44305); Cry1Aa14 (Accession #AAP40639); Cry1Aa15(Accession #AAY66993); Cry1Aa16 (Accession #HQ439776); Cry1Aa17(Accession #HQ439788); Cry1Aa18 (Accession #HQ439790); Cry1Aa19(Accession #HQ685121); Cry1Aa20 (Accession #JF340156); Cry1Aa21(Accession #JN651496); Cry1Aa22 (Accession #KC158223); Cry1Ab1(Accession #AAA22330); Cry1Ab2 (Accession #AAA22613); Cry1Ab3 (Accession#AAA22561); Cry1Ab4 (Accession #BAA00071); Cry1Ab5 (Accession#CAA28405); Cry1Ab6 (Accession #AAA22420); Cry1Ab7 (Accession#CAA31620); Cry1Ab8 (Accession #AAA22551); Cry1Ab9 (Accession#CAA38701); Cry1Ab10 (Accession #A29125); Cry1Ab11 (Accession #I12419);Cry1Ab12 (Accession #AAC64003); Cry1Ab13 (Accession #AAN76494); Cry1Ab14(Accession #AAG16877); Cry1Ab15 (Accession #AA013302); Cry1Ab16(Accession #AAK55546); Cry1Ab17 (Accession #AAT46415); Cry1Ab18(Accession #AAQ88259); Cry1Ab19 (Accession #AAW31761); Cry1Ab20(Accession #ABB72460); Cry1Ab21 (Accession #ABS18384); Cry1Ab22(Accession #ABW87320); Cry1Ab23 (Accession #HQ439777); Cry1Ab24(Accession #HQ439778); Cry1Ab25 (Accession #HQ685122); Cry1Ab26(Accession #HQ847729); Cry1Ab27 (Accession #JN135249); Cry1Ab28(Accession #JN135250); Cry1Ab29 (Accession #JN135251); Cry1Ab30(Accession #JN135252); Cry1Ab31 (Accession #JN135253); Cry1Ab32(Accession #JN135254); Cry1Ab33 (Accession #AAS93798); Cry1Ab34(Accession #KC156668); Cry1Ab-like (Accession #AAK14336); Cry1Ab-like(Accession #AAK14337); Cry1Ab-like (Accession #AAK14338); Cry1Ab-like(Accession #ABG88858); Cry1Ac1 (Accession #AAA22331); Cry1Ac2 (Accession#AAA22338); Cry1Ac3 (Accession #CAA38098); Cry1Ac4 (Accession#AAA73077); Cry1Ac5 (Accession #AAA22339); Cry1Ac6 (Accession#AAA86266); Cry1Ac7 (Accession #AAB46989); Cry1Ac8 (Accession#AAC44841); Cry1Ac9 (Accession #AAB49768); Cry1Ac10 (Accession#CAA05505); Cry1Ac11 (Accession #CAA10270); Cry1Ac12 (Accession#I12418); Cry1Ac13 (Accession #AAD38701); Cry1Ac14 (Accession#AAQ06607); Cry1Ac15 (Accession #AAN07788); Cry1Ac16 (Accession#AAU87037); Cry1Ac17 (Accession #AAX18704); Cry1Ac18 (Accession#AAY88347); Cry1Ac19 (Accession #ABD37053); Cry1Ac20 (Accession#ABB89046); Cry1Ac21 (Accession #AAY66992); Cry1Ac22 (Accession#ABZ01836); Cry1Ac23 (Accession #CAQ30431); Cry1Ac24 (Accession#ABL01535); Cry1Ac25 (Accession #FJ513324); Cry1Ac26 (Accession#FJ617446); Cry1Ac27 (Accession #FJ617447); Cry1Ac28 (Accession#ACM90319); Cry1Ac29 (Accession #DQ438941); Cry1Ac30 (Accession#GQ227507); Cry1Ac31 (Accession #GU446674); Cry1Ac32 (Accession#HM061081); Cry1Ac33 (Accession #GQ866913); Cry1Ac34 (Accession#HQ230364); Cry1Ac35 (Accession #JF340157); Cry1Ac36 (Accession#JN387137); Cry1Ac37 (Accession #JQ317685); Cry1Ad1 (Accession#AAA22340); Cry1Ad2 (Accession #CAA01880); Cry1Ae1 (Accession#AAA22410); Cry1Af1 (Accession #AAB82749); Cry1Ag1 (Accession#AAD46137); Cry1Ah1 (Accession #AAQ14326); Cry1Ah2 (Accession#ABB76664); Cry1Ah3 (Accession #HQ439779); Cry1Ai1 (Accession#AA039719); Cry1Ai2 (Accession #HQ439780); Cry1A-like (Accession#AAK14339); Cry1Ba1 (Accession #CAA29898); Cry1Ba2 (Accession#CAA65003); Cry1Ba3 (Accession #AAK63251); Cry1Ba4 (Accession#AAK51084); Cry1Ba5 (Accession #AB020894); Cry1Ba6 (Accession#ABL60921); Cry1Ba7 (Accession #HQ439781); Cry1Bb1 (Accession#AAA22344); Cry1Bb2 (Accession #HQ439782); Cry1Bc1 (Accession#CAA86568); Cry1Bd1 (Accession #AAD10292); Cry1Bd2 (Accession#AAM93496); Cry1Be1 (Accession #AAC32850); Cry1Be2 (Accession#AAQ52387); Cry1Be3 (Accession #ACV96720); Cry1Be4 (Accession#HM070026); Cry1Bf1 (Accession #CAC50778); Cry1Bf2 (Accession#AAQ52380); Cry1Bg1 (Accession #AA039720); Cry1Bh1 (Accession#HQ589331); Cry1Bi1 (Accession #KC156700); Cry1Ca1 (Accession#CAA30396); Cry1Ca2 (Accession #CAA31951); Cry1Ca3 (Accession#AAA22343); Cry1Ca4 (Accession #CAA01886); Cry1Ca5 (Accession#CAA65457); Cry1Ca6 [1](Accession #AAF37224); Cry1Ca7 (Accession#AAG50438); Cry1Ca8 (Accession #AAM00264); Cry1Ca9 (Accession#AAL79362); Cry1Ca10 (Accession #AAN16462); Cry1Ca11 (Accession#AAX53094); Cry1Ca12 (Accession #HM070027); Cry1Ca13 (Accession#HQ412621); Cry1Ca14 (Accession #JN651493); Cry1Cb1 (Accession #M97880);Cry1Cb2 (Accession #AAG35409); Cry1Cb3 (Accession #ACD50894);Cry1Cb-like (Accession #AAX63901); Cry1Da1 (Accession #CAA38099);Cry1Da2 (Accession #176415); Cry1Da3 (Accession #HQ439784); Cry1Db1(Accession #CAA80234); Cry1Db2 (Accession #AAK48937); Cry1Dc1 (Accession#ABK35074); Cry1Ea1 (Accession #CAA37933); Cry1Ea2 (Accession#CAA39609); Cry1Ea3 (Accession #AAA22345); Cry1Ea4 (Accession#AAD04732); Cry1Ea5 (Accession #A15535); Cry1Ea6 (Accession #AAL50330);Cry1Ea7 (Accession #AAW72936); Cry1Ea8 (Accession #ABX11258); Cry1Ea9(Accession #HQ439785); Cry1Ea10 (Accession #ADR00398); Cry1Ea11(Accession #JQ652456); Cry1Eb1 (Accession #AAA22346); Cry1Fa1 (Accession#AAA22348); Cry1Fa2 (Accession #AAA22347); Cry1Fa3 (Accession#HM070028); Cry1Fa4 (Accession #HM439638); Cry1Fb1 (Accession#CAA80235); Cry1Fb2 (Accession #BAA25298); Cry1Fb3 (Accession#AAF21767); Cry1Fb4 (Accession #AAC10641); Cry1Fb5 (Accession#AA013295); Cry1Fb6 (Accession #ACD50892); Cry1Fb7 (Accession#ACD50893); Cry1Ga1 (Accession #CAA80233); Cry1Ga2 (Accession#CAA70506); Cry1Gb1 (Accession #AAD10291); Cry1Gb2 (Accession#AA013756); Cry1Gc1 (Accession #AAQ52381); Cry1Ha1 (Accession#CAA80236); Cry1Hb1 (Accession #AAA79694); Cry1Hb2 (Accession#HQ439786); Cry1H-like (Accession #AAF01213); Cry1Ia1 (Accession#CAA44633); Cry1Ia2 (Accession #AAA22354); Cry1Ia3 (Accession#AAC36999); Cry1Ia4 (Accession #AAB00958); Cry1Ia5 (Accession#CAA70124); Cry1Ia6 (Accession #AAC26910); Cry1Ia7 (Accession#AAM73516); Cry1Ia8 (Accession #AAK66742); Cry1Ia9 (Accession#AAQ08616); Cry1Ia10 (Accession #AAP86782); Cry1Ia11 (Accession#CAC85964); Cry1Ia12 (Accession #AAV53390); Cry1Ia13 (Accession#ABF83202); Cry1Ia14 (Accession #ACG63871); Cry1Ia15 (Accession#FJ617445); Cry1Ia16 (Accession #FJ617448); Cry1Ia17 (Accession#GU989199); Cry1Ia18 (Accession #ADK23801); Cry1Ia19 (Accession#HQ439787); Cry1Ia20 (Accession #JQ228426); Cry1Ia21 (Accession#JQ228424); Cry1Ia22 (Accession #JQ228427); Cry1Ia23 (Accession#JQ228428); Cry1Ia24 (Accession #JQ228429); Cry1Ia25 (Accession#JQ228430); Cry1Ia26 (Accession #JQ228431); Cry1Ia27 (Accession#JQ228432); Cry1Ia28 (Accession #JQ228433); Cry1Ia29 (Accession#JQ228434); Cry1Ia30 (Accession #JQ317686); Cry1Ia31 (Accession#JX944038); Cry1Ia32 (Accession #JX944039); Cry1Ia33 (Accession#JX944040); Cry1Ib1 (Accession #AAA82114); Cry1Ib2 (Accession#ABW88019); Cry1Ib3 (Accession #ACD75515); Cry1Ib4 (Accession#HM051227); Cry1Ib5 (Accession #HM070028); Cry1Ib6 (Accession#ADK38579); Cry1Ib7 (Accession #JN571740); Cry1Ib8 (Accession#JN675714); Cry1Ib9 (Accession #JN675715); Cry1Ib10 (Accession#JN675716); Cry1Ib11 (Accession #JQ228423); Cry1Ic1 (Accession#AAC62933); Cry1Ic2 (Accession #AAE71691); Cry1Id1 (Accession#AAD44366); Cry1Id2 (Accession #JQ228422); Cry1Ie1 (Accession#AAG43526); Cry1Ie2 (Accession #HM439636); Cry1Ie3 (Accession#KC156647); Cry1Ie4 (Accession #KC156681); Cry1If1 (Accession#AAQ52382); Cry1Ig1 (Accession #KC156701); Cry1I-like (Accession#AAC31094); Cry1I-like (Accession #ABG88859); Cry1Ja1 (Accession#AAA22341); Cry1Ja2 (Accession #HM070030); Cry1Ja3 (Accession#JQ228425); Cry1Jb1 (Accession #AAA98959); Cry1Jc1 (Accession#AAC31092); Cry1Jc2 (Accession #AAQ52372); Cry1Jd1 (Accession#CAC50779); Cry1Ka1 (Accession #AAB00376); Cry1Ka2 (Accession#HQ439783); Cry1La1 (Accession #AAS60191); Cry1La2 (Accession#HM070031); Cry1Ma1 (Accession #FJ884067); Cry1Ma2 (Accession#KC156659); Cry1Na1 (Accession #KC156648); Cry1Nb1 (Accession#KC156678); Cry1-like (Accession #AAC31091); Cry2Aa1 (Accession#AAA22335); Cry2Aa2 (Accession #AAA83516); Cry2Aa3 (Accession #D86064);Cry2Aa4 (Accession #AAC04867); Cry2Aa5 (Accession #CAA10671); Cry2Aa6(Accession #CAA10672); Cry2Aa7 (Accession #CAA10670); Cry2Aa8 (Accession#AA013734); Cry2Aa9 (Accession #AAO13750); Cry2Aa10 (Accession#AAQ04263); Cry2Aa11 (Accession #AAQ52384); Cry2Aa12 (Accession#ABI83671); Cry2Aa13 (Accession #ABL01536); Cry2Aa14 (Accession#ACF04939); Cry2Aa15 (Accession #JN426947); Cry2Ab1 (Accession#AAA22342); Cry2Ab2 (Accession #CAA39075); Cry2Ab3 (Accession#AAG36762); Cry2Ab4 (Accession #AA013296); Cry2Ab5 (Accession#AAQ04609); Cry2Ab6 (Accession #AAP59457); Cry2Ab7 (Accession#AAZ66347); Cry2Ab8 (Accession #ABC95996); Cry2Ab9 (Accession#ABC74968); Cry2Ab10 (Accession #EF157306); Cry2Ab11 (Accession#CAM84575); Cry2Ab12 (Accession #ABM21764); Cry2Ab13 (Accession#ACG76120); Cry2Ab14 (Accession #ACG76121); Cry2Ab15 (Accession#HM037126); Cry2Ab16 (Accession #GQ866914); Cry2Ab17 (Accession#HQ439789); Cry2Ab18 (Accession #JN135255); Cry2Ab19 (Accession#JN135256); Cry2Ab20 (Accession #JN135257); Cry2Ab21 (Accession#JN135258); Cry2Ab22 (Accession #JN135259); Cry2Ab23 (Accession#JN135260); Cry2Ab24 (Accession #JN135261); Cry2Ab25 (Accession#JN415485); Cry2Ab26 (Accession #JN426946); Cry2Ab27 (Accession#JN415764); Cry2Ab28 (Accession #JN651494); Cry2Ac1 (Accession#CAA40536); Cry2Ac2 (Accession #AAG35410); Cry2Ac3 (Accession#AAQ52385); Cry2Ac4 (Accession #ABC95997); Cry2Ac5 (Accession#ABC74969); Cry2Ac6 (Accession #ABC74793); Cry2Ac7 (Accession#CAL18690); Cry2Ac8 (Accession #CAM09325); Cry2Ac9 (Accession#CAM09326); Cry2Ac10 (Accession #ABN15104); Cry2Ac11 (Accession#CAM83895); Cry2Ac12 (Accession #CAM83896); Cry2Ad1 (Accession#AAF09583); Cry2Ad2 (Accession #ABC86927); Cry2Ad3 (Accession#CAK29504); Cry2Ad4 (Accession #CAM32331); Cry2Ad5 (Accession#CA078739); Cry2Ae1 (Accession #AAQ52362); Cry2Af1 (Accession#AB030519); Cry2Af2 (Accession #GQ866915); Cry2Ag1 (Accession#ACH91610); Cry2Ah1 (Accession #EU939453); Cry2Ah2 (Accession#ACL80665); Cry2Ah3 (Accession #GU073380); Cry2Ah4 (Accession#KC156702); Cry2Ai1 (Accession #FJ788388); Cry2Aj (Accession #); Cry2Ak1(Accession #KC156660); Cry2Ba1 (Accession #KC156658); Cry3Aa1 (Accession#AAA22336); Cry3Aa2 (Accession #AAA22541); Cry3Aa3 (Accession#CAA68482); Cry3Aa4 (Accession #AAA22542); Cry3Aa5 (Accession#AAA50255); Cry3Aa6 (Accession #AAC43266); Cry3Aa7 (Accession#CAB41411); Cry3Aa8 (Accession #AAS79487); Cry3Aa9 (Accession#AAW05659); Cry3Aa10 (Accession #AAU29411); Cry3Aa11 (Accession#AAW82872); Cry3Aa12 (Accession #ABY49136); Cry3Ba1 (Accession#CAA34983); Cry3Ba2 (Accession #CAA00645); Cry3Ba3 (Accession#JQ397327); Cry3Bb1 (Accession #AAA22334); Cry3Bb2 (Accession#AAA74198); Cry3Bb3 (Accession #115475); Cry3Ca1 (Accession #CAA42469);Cry4Aa1 (Accession #CAA68485); Cry4Aa2 (Accession #BAA00179); Cry4Aa3(Accession #CAD30148); Cry4Aa4 (Accession #AFB18317); Cry4A-like(Accession #AAY96321); Cry4Ba1 (Accession #CAA30312); Cry4Ba2 (Accession#CAA30114); Cry4Ba3 (Accession #AAA22337); Cry4Ba4 (Accession#BAA00178); Cry4Ba5 (Accession #CAD30095); Cry4Ba-like (Accession#ABC47686); Cry4Ca1 (Accession #EU646202); Cry4Cb1 (Accession#FJ403208); Cry4Cb2 (Accession #FJ597622); Cry4Cc1 (Accession#FJ403207); Cry5Aa1 (Accession #AAA67694); Cry5Ab1 (Accession#AAA67693); Cry5Ac1 (Accession #134543); Cry5Ad1 (Accession #ABQ82087);Cry5Ba1 (Accession #AAA68598); Cry5Ba2 (Accession #ABW88931); Cry5Ba3(Accession #AFJ04417); Cry5Ca1 (Accession #HM461869); Cry5Ca2 (Accession#ZP_04123426); Cry5Da1 (Accession #HM461870); Cry5Da2 (Accession#ZP_04123980); Cry5Ea1 (Accession #HM485580); Cry5Ea2 (Accession#ZP_04124038); Cry6Aa1 (Accession #AAA22357); Cry6Aa2 (Accession#AAM46849); Cry6Aa3 (Accession #ABH03377); Cry6Ba1 (Accession#AAA22358); Cry7Aa1 (Accession #AAA22351); Cry7Ab1 (Accession#AAA21120); Cry7Ab2 (Accession #AAA21121); Cry7Ab3 (Accession#ABX24522); Cry7Ab4 (Accession #EU380678); Cry7Ab5 (Accession#ABX79555); Cry7Ab6 (Accession #ACI44005); Cry7Ab7 (Accession#ADB89216); Cry7Ab8 (Accession #GU145299); Cry7Ab9 (Accession#ADD92572); Cry7Ba1 (Accession #ABB70817); Cry7Bb1 (Accession#KC156653); Cry7Ca1 (Accession #ABR67863); Cry7Cb1 (Accession#KC156698); Cry7Da1 (Accession #ACQ99547); Cry7Da2 (Accession#HM572236); Cry7Da3 (Accession #KC156679); Cry7Ea1 (Accession#HM035086); Cry7Ea2 (Accession #HM132124); Cry7Ea3 (Accession#EEM19403); Cry7Fa1 (Accession #HM035088); Cry7Fa2 (Accession#EEM19090); Cry7Fb1 (Accession #HM572235); Cry7Fb2 (Accession#KC156682); Cry7Ga1 (Accession #HM572237); Cry7Ga2 (Accession#KC156669); Cry7Gb1 (Accession #KC156650); Cry7Gc1 (Accession#KC156654); Cry7Gd1 (Accession #KC156697); Cry7Ha1 (Accession#KC156651); Cry71a1 (Accession #KC156665); Cry7Ja1 (Accession#KC156671); Cry7Ka1 (Accession #KC156680); Cry7Kb1 (Accession#BAM99306); Cry7La1 (Accession #BAM99307); Cry8Aa1 (Accession#AAA21117); Cry8Ab1 (Accession #EU044830); Cry8Ac1 (Accession#KC156662); Cry8Ad1 (Accession #KC156684); Cry8Ba1 (Accession#AAA21118); Cry8Bb1 (Accession #CAD57542); Cry8Bc1 (Accession#CAD57543); Cry8Ca1 (Accession #AAA21119); Cry8Ca2 (Accession#AAR98783); Cry8Ca3 (Accession #EU625349); Cry8Ca4 (Accession#ADB54826); Cry8Da1 (Accession #BAC07226); Cry8Da2 (Accession#BD133574); Cry8Da3 (Accession #BD133575); Cry8Db1 (Accession#BAF93483); Cry8Ea1 (Accession #AAQ73470); Cry8Ea2 (Accession#EU047597); Cry8Ea3 (Accession #KC855216); Cry8Fa1 (Accession#AAT48690); Cry8Fa2 (Accession #HQ174208); Cry8Fa3 (Accession#AFH78109); Cry8Ga1 (Accession #AAT46073); Cry8Ga2 (Accession#ABC42043); Cry8Ga3 (Accession #FJ198072); Cry8Ha1 (Accession#AAW81032); Cry8Ia1 (Accession #EU381044); Cry8Ia2 (Accession#GU073381); Cry8Ia3 (Accession #HM044664); Cry8Ia4 (Accession#KC156674); Cry8Ib1 (Accession #GU325772); Cry8Ib2 (Accession#KC156677); Cry8Ja1 (Accession #EU625348); Cry8Ka1 (Accession#FJ422558); Cry8Ka2 (Accession #ACN87262); Cry8Kb1 (Accession#HM123758); Cry8Kb2 (Accession #KC156675); Cry8La1 (Accession#GU325771); Cry8Ma1 (Accession #HM044665); Cry8Ma2 (Accession#EEM86551); Cry8Ma3 (Accession #HM210574); Cry8Na1 (Accession#HM640939); Cry8Pa1 (Accession #HQ388415); Cry8Qa1 (Accession#HQ441166); Cry8Qa2 (Accession #KC152468); Cry8Ra1 (Accession#AFP87548); Cry8Sa1 (Accession #JQ740599); Cry8Ta1 (Accession#KC156673); Cry8-like (Accession #FJ770571); Cry8-like (Accession#ABS53003); Cry9Aa1 (Accession #CAA41122); Cry9Aa2 (Accession#CAA41425); Cry9Aa3 (Accession #GQ249293); Cry9Aa4 (Accession#GQ249294); Cry9Aa5 (Accession #JX174110); Cry9Aa like (Accession#AAQ52376); Cry9Ba1 (Accession #CAA52927); Cry9Ba2 (Accession#GU299522); Cry9Bb1 (Accession #AAV28716); Cry9Ca1 (Accession#CAA85764); Cry9Ca2 (Accession #AAQ52375); Cry9Da1 (Accession#BAA19948); Cry9Da2 (Accession #AAB97923); Cry9Da3 (Accession#GQ249293); Cry9Da4 (Accession #GQ249297); Cry9Db1 (Accession#AAX78439); Cry9Dc1 (Accession #KC156683); Cry9Ea1 (Accession#BAA34908); Cry9Ea2 (Accession #AA012908); Cry9Ea3 (Accession#ABM21765); Cry9Ea4 (Accession #ACE88267); Cry9Ea5 (Accession#ACF04743); Cry9Ea6 (Accession #ACG63872); Cry9Ea7 (Accession#FJ380927); Cry9Ea8 (Accession #GQ249292); Cry9Ea9 (Accession#JN651495); Cry9Eb1 (Accession #CAC50780); Cry9Eb2 (Accession#GQ249298); Cry9Eb3 (Accession #KC156646); Cry9Ec1 (Accession#AAC63366); Cry9Ed1 (Accession #AAX78440); Cry9Ee1 (Accession#GQ249296); Cry9Ee2 (Accession #KC156664); Cry9Fa1 (Accession#KC156692); Cry9Ga1 (Accession #KC156699); Cry9-like (Accession#AAC63366); Cry10Aa1 (Accession #AAA22614); Cry10Aa2 (Accession#E00614); Cry10Aa3 (Accession #CAD30098); Cry10Aa4 (Accession#AFB18318); Cry10A-like (Accession #DQ167578); Cry11Aa1 (Accession#AAA22352); Cry11Aa2 (Accession #AAA22611); Cry11Aa3 (Accession#CAD30081); Cry11Aa4 (Accession #AFB18319); Cry11Aa-like (Accession#DQ166531); Cry11Ba1 (Accession #CAA60504); Cry11Bb1 (Accession#AAC97162); Cry11Bb2 (Accession #HM068615); Cry12Aa1 (Accession#AAA22355); Cry13Aa1 (Accession #AAA22356); Cry14Aa1 (Accession#AAA21516); Cry14Ab1 (Accession #KC156652); Cry15Aa1 (Accession#AAA22333); Cry16Aa1 (Accession #CAA63860); Cry17Aa1 (Accession#CAA67841); Cry18Aa1 (Accession #CAA67506); Cry18Ba1 (Accession#AAF89667); Cry18Ca1 (Accession #AAF89668); Cry19Aa1 (Accession#CAA68875); Cry19Ba1 (Accession #BAA32397); Cry19Ca1 (Accession#AFM37572); Cry20Aa1 (Accession #AAB93476); Cry20Ba1 (Accession#ACS93601); Cry20Ba2 (Accession #KC156694); Cry20-like (Accession#GQ144333); Cry21Aa1 (Accession #I32932); Cry21Aa2 (Accession #I66477);Cry21Ba1 (Accession #BAC06484); Cry21Ca1 (Accession #JF521577); Cry21Ca2(Accession #KC156687); Cry21Da1 (Accession #JF521578); Cry22Aa1(Accession #I34547); Cry22Aa2 (Accession #CAD43579); Cry22Aa3 (Accession#ACD93211); Cry22Ab1 (Accession #AAK50456); Cry22Ab2 (Accession#CAD43577); Cry22Ba1 (Accession #CAD43578); Cry22Bb1 (Accession#KC156672); Cry23Aa1 (Accession #AAF76375); Cry24Aa1 (Accession#AAC61891); Cry24Ba1 (Accession #BAD32657); Cry24Ca1 (Accession#CAJ43600); Cry25Aa1 (Accession #AAC61892); Cry26Aa1 (Accession#AAD25075); Cry27Aa1 (Accession #BAA82796); Cry28Aa1 (Accession#AAD24189); Cry28Aa2 (Accession #AAG00235); Cry29Aa1 (Accession#CAC80985); Cry30Aa1 (Accession #CAC80986); Cry30Ba1 (Accession#BAD00052); Cry30Ca1 (Accession #BAD67157); Cry30Ca2 (Accession#ACU24781); Cry30Da1 (Accession #EF095955); Cry30Db1 (Accession#BAE80088); Cry30Ea1 (Accession #ACC95445); Cry30Ea2 (Accession#FJ499389); Cry30Fa1 (Accession #ACI22625); Cry30Ga1 (Accession#ACG60020); Cry30Ga2 (Accession #HQ638217); Cry31Aa1 (Accession#BAB11757); Cry31Aa2 (Accession #AAL87458); Cry31Aa3 (Accession#BAE79808); Cry31Aa4 (Accession #BAF32571); Cry31Aa5 (Accession#BAF32572); Cry31Aa6 (Accession #BA144026); Cry31Ab1 (Accession#BAE79809); Cry31Ab2 (Accession #BAF32570); Cry31Ac1 (Accession#BAF34368); Cry31Ac2 (Accession #AB731600); Cry31Ad1 (Accession#BA144022); Cry32Aa1 (Accession #AAG36711); Cry32Aa2 (Accession#GU063849); Cry32Ab1 (Accession #GU063850); Cry32Ba1 (Accession#BAB78601); Cry32Ca1 (Accession #BAB78602); Cry32Cb1 (Accession#KC156708); Cry32Da1 (Accession #BAB78603); Cry32Ea1 (Accession#GU324274); Cry32Ea2 (Accession #KC156686); Cry32Eb1 (Accession#KC156663); Cry32Fa1 (Accession #KC156656); Cry32Ga1 (Accession#KC156657); Cry32Ha1 (Accession #KC156661); Cry32Hb1 (Accession#KC156666); Cry32Ia1 (Accession #KC156667); Cry32Ja1 (Accession#KC156685); Cry32Ka1 (Accession #KC156688); Cry32La1 (Accession#KC156689); Cry32Ma1 (Accession #KC156690); Cry32Mb1 (Accession#KC156704); Cry32Na1 (Accession #KC156691); Cry32Oa1 (Accession#KC156703); Cry32Pa1 (Accession #KC156705); Cry32Qa1 (Accession#KC156706); Cry32Ra1 (Accession #KC156707); Cry32Sa1 (Accession#KC156709); Cry32Ta1 (Accession #KC156710); Cry32Ua1 (Accession#KC156655); Cry33Aa1 (Accession #AAL26871); Cry34Aa1 (Accession#AAG50341); Cry34Aa2 (Accession #AAK64560); Cry34Aa3 (Accession#AAT29032); Cry34Aa4 (Accession #AAT29030); Cry34Ab1 (Accession#AAG41671); Cry34Ac1 (Accession #AAG50118); Cry34Ac2 (Accession#AAK64562); Cry34Ac3 (Accession #AAT29029); Cry34Ba1 (Accession#AAK64565); Cry34Ba2 (Accession #AAT29033); Cry34Ba3 (Accession#AAT29031); Cry35Aa1 (Accession #AAG50342); Cry35Aa2 (Accession#AAK64561); Cry35Aa3 (Accession #AAT29028); Cry35Aa4 (Accession#AAT29025); Cry35Ab1 (Accession #AAG41672); Cry35Ab2 (Accession#AAK64563); Cry35Ab3 (Accession #AY536891); Cry35Ac1 (Accession#AAG50117); Cry35Ba1 (Accession #AAK64566); Cry35Ba2 (Accession#AAT29027); Cry35Ba3 (Accession #AAT29026); Cry36Aa1 (Accession#AAK64558); Cry37Aa1 (Accession #AAF76376); Cry38Aa1 (Accession#AAK64559); Cry39Aa1 (Accession #BAB72016); Cry40Aa1 (Accession#BAB72018); Cry40Ba1 (Accession #BAC77648); Cry40Ca1 (Accession#EU381045); Cry40Da1 (Accession #ACF15199); Cry41Aa1 (Accession#BAD35157); Cry41Ab1 (Accession #BAD35163); Cry41Ba1 (Accession#HM461871); Cry41Ba2 (Accession #ZP_04099652); Cry42Aa1 (Accession#BAD35166); Cry43Aa1 (Accession #BAD15301); Cry43Aa2 (Accession#BAD95474); Cry43Ba1 (Accession #BAD15303); Cry43Ca1 (Accession#KC156676); Cry43Cb1 (Accession #KC156695); Cry43Cc1 (Accession#KC156696); Cry43-like (Accession #BAD15305); Cry44Aa (Accession#BAD08532); Cry45Aa (Accession #BAD22577); Cry46Aa (Accession#BAC79010); Cry46Aa2 (Accession #BAG68906); Cry46Ab (Accession#BAD35170); Cry47Aa (Accession #AAY24695); Cry48Aa (Accession#CAJ18351); Cry48Aa2 (Accession #CAJ86545); Cry48Aa3 (Accession#CAJ86546); Cry48Ab (Accession #CAJ86548); Cry48Ab2 (Accession#CAJ86549); Cry49Aa (Accession #CAH56541); Cry49Aa2 (Accession#CAJ86541); Cry49Aa3 (Accession #CAJ86543); Cry49Aa4 (Accession#CAJ86544); Cry49Ab1 (Accession #CAJ86542); Cry50Aa1 (Accession#BAE86999); Cry50Ba1 (Accession #GU446675); Cry50Ba2 (Accession#GU446676); Cry51Aa1 (Accession #AB114444); Cry51Aa2 (Accession#GU570697); Cry52Aa1 (Accession #EF613489); Cry52Ba1 (Accession#FJ361760); Cry53Aa1 (Accession #EF633476); Cry53Ab1 (Accession#FJ361759); Cry54Aa1 (Accession #ACA52194); Cry54Aa2 (Accession#GQ140349); Cry54Ba1 (Accession #GU446677); Cry55Aa1 (Accession#ABW88932); Cry54Ab1 (Accession #JQ916908); Cry55Aa2 (Accession#AAE33526); Cry56Aa1 (Accession #ACU57499); Cry56Aa2 (Accession#GQ483512); Cry56Aa3 (Accession #JX025567); Cry57Aa1 (Accession#ANC87261); Cry58Aa1 (Accession #ANC87260); Cry59Ba1 (Accession#JN790647); Cry59Aa1 (Accession #ACR43758); Cry60Aa1 (Accession#ACU24782); Cry60Aa2 (Accession #EA057254); Cry60Aa3 (Accession#EEM99278); Cry60Ba1 (Accession #GU810818); Cry60Ba2 (Accession#EA057253); Cry60Ba3 (Accession #EEM99279); Cry61Aa1 (Accession#HM035087); Cry61Aa2 (Accession #HM132125); Cry61Aa3 (Accession#EEM19308); Cry62Aa1 (Accession #HM054509); Cry63Aa1 (Accession#BAI44028); Cry64Aa1 (Accession #BAJ05397); Cry65Aa1 (Accession#HM461868); Cry65Aa2 (Accession #ZP_04123838); Cry66Aa1 (Accession#HM485581); Cry66Aa2 (Accession #ZP_04099945); Cry67Aa1 (Accession#HM485582); Cry67Aa2 (Accession #ZP_04148882); Cry68Aa1 (Accession#HQ113114); Cry69Aa1 (Accession #HQ401006); Cry69Aa2 (Accession#JQ821388); Cry69Ab1 (Accession #JN209957); Cry70Aa1 (Accession#JN646781); Cry70Ba1 (Accession #ADO51070); Cry70Bb1 (Accession#EEL67276); Cry71Aa1 (Accession #JX025568); Cry72Aa1 (Accession#JX025569); Cyt1Aa (GenBank Accession Number X03182); Cyt1Ab (GenBankAccession Number X98793); Cyt1B (GenBank Accession Number U37196); Cyt2A(GenBank Accession Number Z14147); and Cyt2B (GenBank Accession NumberU52043).

Examples of δ-endotoxins also include but are not limited to Cry1Aproteins of U.S. Pat. Nos. 5,880,275, 7,858,849 8,530,411, 8,575,433,and 8,686,233; a DIG-3 or DIG-11 toxin (N-terminal deletion of a-helix 1and/or a-helix 2 variants of cry proteins such as Cry1A, Cry3A) of U.S.Pat. Nos. 8,304,604, 8,304,605 and 8,476,226; Cry1B of U.S. patentapplication Ser. No. 10/525,318; Cry1C of U.S. Pat. No. 6,033,874; Cry1Fof U.S. Pat. Nos. 5,188,960 and 6,218,188; Cry1A/F chimeras of U.S. Pat.Nos. 7,070,982; 6,962,705 and 6,713,063); a Cry2 protein such as Cry2Abprotein of U.S. Pat. No. 7,064,249); a Cry3A protein including but notlimited to an engineered hybrid insecticidal protein (eHIP) created byfusing unique combinations of variable regions and conserved blocks ofat least two different Cry proteins (US Patent Application PublicationNumber 2010/0017914); a Cry4 protein; a Cry5 protein; a Cry6 protein;Cry8 proteins of U.S. Pat. Nos. 7,329,736, 7,449,552, 7,803,943,7,476,781, 7,105,332, 7,378,499 and 7,462,760; a Cry9 protein such assuch as members of the Cry9A, Cry9B, Cry9C, Cry9D, Cry9E and Cry9Ffamilies, including but not limited to the Cry9D protein of U.S. Pat.No. 8,802,933 and the Cry9B protein of U.S. Pat. No. 8,802,934; a Cry15protein of Naimov, et al., (2008) Applied and EnvironmentalMicrobiology, 74:7145-7151; a Cry22, a Cry34Ab1 protein of U.S. Pat.Nos. 6,127,180, 6,624,145 and 6,340,593; a CryET33 and CryET34 proteinof U.S. Pat. Nos. 6,248,535, 6,326,351, 6,399,330, 6,949,626, 7,385,107and 7,504,229; a CryET33 and CryET34 homologs of US Patent PublicationNumber 2006/0191034, 2012/0278954, and PCT Publication Number WO2012/139004; a Cry35Ab1 protein of U.S. Pat. Nos. 6,083,499, 6,548,291and 6,340,593; a Cry46 protein, a Cry 51 protein, a Cry binary toxin; aTIC807 of US Patent Application Publication Number 2008/0295207; ET29,ET37, TIC809, TIC810, TIC812, TIC127, TIC128 of PCT US 2006/033867;TIC853 toxins of U.S. Pat. No. 8,513,494; TIC3131, TIC 3400, and TIC3407of US Patent Application Publication Number 2015/0047076; AXMI-027,AXMI-036, and AXMI-038 of U.S. Pat. No. 8,236,757; AXMI-031, AXMI-039,AXMI-040, AXMI-049 of U.S. Pat. No. 7,923,602; AXMI-018, AXMI-020 andAXMI-021 of WO 2006/083891; AXMI-010 of WO 2005/038032; AXMI-003 of WO2005/021585; AXMI-008 of US Patent Application Publication Number2004/0250311; AXMI-006 of US Patent Application Publication Number2004/0216186; AXMI-007 of US Patent Application Publication Number2004/0210965; AXMI-009 of US Patent Application Number 2004/0210964;AXMI-014 of US Patent Application Publication Number 2004/0197917;AXMI-004 of US Patent Application Publication Number 2004/0197916;AXMI-028 and AXMI-029 of WO 2006/119457; AXMI-007, AXMI-008,AXMI-0080rf2, AXMI-009, AXMI-014 and AXMI-004 of WO 2004/074462;AXMI-150 of U.S. Pat. No. 8,084,416; AXMI-205 of US Patent ApplicationPublication Number 2011/0023184; AXMI-011, AXMI-012, AXMI-013, AXMI-015,AXMI-019, AXMI-044, AXMI-037, AXMI-043, AXMI-033, AXMI-034, AXMI-022,AXMI-023, AXMI-041, AXMI-063 and AXMI-064 of US Patent ApplicationPublication Number 2011/0263488; AXMI-R1 and related proteins of USPatent Application Publication Number 2010/0197592; AXMI221Z, AXMI222z,AXMI223z, AXMI224z and AXMI225z of WO 2011/103248; AXMI218, AXMI219,AXMI220, AXMI226, AXMI227, AXMI228, AXMI229, AXMI230 and AXMI231 of WO2011/103247 and U.S. Pat. No. 8,759,619; AXMI-115, AXMI-113, AXMI-005,AXMI-163 and AXMI-184 of U.S. Pat. No. 8,334,431; AXMI-001, AXMI-002,AXMI-030, AXMI-035 and AXMI-045 of US Patent Application PublicationNumber 2010/0298211; AXMI-066 and AXMI-076 of US Patent ApplicationPublication Number 2009/0144852; AXMI128, AXMI130, AXMI131, AXMI133,AXMI140, AXMI141, AXMI142, AXMI143, AXMI144, AXMI146, AXMI148, AXMI149,AXMI152, AXMI153, AXMI154, AXMI155, AXMI156, AXMI157, AXMI158, AXMI162,AXMI165, AXMI166, AXMI167, AXMI168, AXMI169, AXMI170, AXMI171, AXMI172,AXMI173, AXMI174, AXMI175, AXMI176, AXMI177, AXMI178, AXMI179, AXMI180,AXMI181, AXMI182, AXMI185, AXMI186, AXMI187, AXMI188, AXMI189 of U.S.Pat. No. 8,318,900; AXMI079, AXMI080, AXMI081, AXMI082, AXMI091,AXMI092, AXMI096, AXMI097, AXMI098, AXMI099, AXMI100, AXMI101, AXMI102,AXMI103, AXMI104, AXMI107, AXMI108, AXMI109, AXMI110, AXMI111, AXMI112,AXMI114, AXMI116, AXMI117, AXMI118, AXMI119, AXMI120, AXMI121, AXMI122,AXMI123, AXMI124, AXMI1257, AXMI1268, AXMI127, AXMI129, AXMI164,AXMI151, AXMI161, AXMI183, AXMI132, AXMI138, AXMI137 of US PatentApplication Publication Number 2010/0005543, AXMI270 of US PatentApplication Publication US20140223598, AXMI279 of US Patent ApplicationPublication US20140223599, cry proteins such as Cry1A and Cry3A havingmodified proteolytic sites of U.S. Pat. No. 8,319,019; a Cry1Ac, Cry2Aaand Cry1Ca toxin protein from Bacillus thuringiensis strain VBTS 2528 ofUS Patent Application Publication Number 2011/0064710. Other Cryproteins are well known to one skilled in the art (see, Crickmore, etal., “Bacillus thuringiensis toxin nomenclature”(2011), atlifesci.sussex.ac.uk/home/Neil_Crickmore/Bt/which can be accessed on theworld-wide web using the “www”prefix). The insecticidal activity of Cryproteins is well known to one skilled in the art (for review, see, vanFrannkenhuyzen, (2009) J. Invert. Path. 101:1-16). The use of Cryproteins as transgenic plant traits is well known to one skilled in theart and Cry-transgenic plants including but not limited to plantsexpressing Cry1Ac, Cry1Ac+Cry2Ab, Cry1Ab, Cry1A.105, Cry1F, Cry1Fa2,Cry1F+Cry1Ac, Cry2Ab, Cry3A, mCry3A, Cry3Bb1, Cry34Ab1, Cry35Ab1, Vip3A,mCry3A, Cry9c and CBI-Bt have received regulatory approval (see,Sanahuja, (2011) Plant Biotech Journal 9:283-300 and the CERA (2010) GMCrop Database Center for Environmental Risk Assessment (CERA), ILSIResearch Foundation, Washington D.C. atcera-gmc.org/index.php?action=gm_crop_database, which can be accessed onthe world-wide web using the “www”prefix). More than one pesticidalproteins well known to one skilled in the art can also be expressed inplants such as Vip3Ab & Cry1Fa (US2012/0317682); Cry1BE & Cry1F(US2012/0311746); Cry1CA & Cry1AB (US2012/0311745); Cry1F & CryCa(US2012/0317681); Cry1DA & Cry1BE (US2012/0331590); Cry1DA & Cry1Fa(US2012/0331589); Cry1AB & Cry1BE (US2012/0324606); Cry1Fa & Cry2Aa andCry1I & Cry1E (US2012/0324605); Cry34Ab/35Ab and Cry6Aa (US20130167269);Cry34Ab/VCry35Ab & Cry3Aa (US20130167268); Cry1Ab & Cry1F(US20140182018); and Cry3A and Cry1Ab or Vip3Aa (US20130116170).Pesticidal proteins also include insecticidal lipases including lipidacyl hydrolases of U.S. Pat. No. 7,491,869, and cholesterol oxidasessuch as from Streptomyces (Purcell et al. (1993) Biochem Biophys ResCommun 15:1406-1413). Pesticidal proteins also include VIP (vegetativeinsecticidal proteins) toxins of U.S. Pat. Nos. 5,877,012, 6,107,2796,137,033, 7,244,820, 7,615,686, and 8,237,020 and the like. Other VIPproteins are well known to one skilled in the art (see,lifesci.sussex.ac.uk/home/Neil_Crickmore/Bt/vip.html which can beaccessed on the world-wide web using the “www” prefix). Pesticidalproteins also include toxin complex (TC) proteins, obtainable fromorganisms such as Xenorhabdus, Photorhabdus and Paenibacillus (see, U.S.Pat. Nos. 7,491,698 and 8,084,418). Some TC proteins have “stand alone”insecticidal activity and other TC proteins enhance the activity of thestand-alone toxins produced by the same given organism. The toxicity ofa “stand-alone” TC protein (from Photorhabdus, Xenorhabdus orPaenibacillus, for example) can be enhanced by one or more TC protein“potentiators” derived from a source organism of a different genus.There are three main types of TC proteins. As referred to herein, ClassA proteins (“Protein A”) are stand-alone toxins. Class B proteins(“Protein B”) and Class C proteins (“Protein C”) enhance the toxicity ofClass A proteins. Examples of Class A proteins are TcbA, TcdA, XptA1 andXptA2. Examples of Class B proteins are TcaC, TcdB, XptB1Xb and XptC1Wi.Examples of Class C proteins are TccC, XptC1Xb and XptB1Wi. Pesticidalproteins also include spider, snake and scorpion venom proteins.Examples of spider venom peptides include but not limited to lycotoxin-1peptides and mutants thereof (U.S. Pat. No. 8,334,366).

One aspect pertains to isolated or recombinant nucleic acid moleculescomprising nucleic acid sequences encoding PIP-72 polypeptides and asilencing element. As used herein, the term “nucleic acid molecule”refers to DNA molecules (e.g., recombinant DNA, cDNA, genomic DNA,plastid DNA, mitochondrial DNA) and RNA molecules (e.g., mRNA) andanalogs of the DNA or RNA generated using nucleotide analogs. Thenucleic acid molecule can be single-stranded or double-stranded, butpreferably is double-stranded DNA.

An “isolated” nucleic acid molecule (or DNA) is used herein to refer toa nucleic acid sequence (or DNA) that is no longer in its naturalenvironment, for example in vitro. A “recombinant” nucleic acid molecule(or DNA) is used herein to refer to a nucleic acid sequence (or DNA)that is in a recombinant bacterial or plant host cell. In someembodiments, an “isolated” or “recombinant” nucleic acid is free ofsequences (preferably protein encoding sequences) that naturally flankthe nucleic acid (i.e., sequences located at the 5′ and 3′ ends of thenucleic acid) in the genomic DNA of the organism from which the nucleicacid is derived. For purposes of the disclosure, “isolated” or“recombinant” when used to refer to nucleic acid molecules excludesisolated chromosomes. For example, in various embodiments, therecombinant nucleic acid molecule encoding a PIP-72 polypeptide cancontain less than about 5 kb, 4 kb, 3 kb, 2 kb, 1 kb, 0.5 kb or 0.1 kbof nucleic acid sequences that naturally flank the nucleic acid moleculein genomic DNA of the cell from which the nucleic acid is derived.

In some embodiments an isolated nucleic acid molecule encoding a PIP-72polypeptide has one or more change in the nucleic acid sequence comparedto the native or genomic nucleic acid sequence. In some embodiments thechange in the native or genomic nucleic acid sequence includes but isnot limited to: changes in the nucleic acid sequence due to thedegeneracy of the genetic code; changes in the nucleic acid sequence dueto the amino acid substitution, insertion, deletion and/or additioncompared to the native or genomic sequence; removal of one or moreintron; deletion of one or more upstream or downstream regulatoryregions; and deletion of the 5′ and/or 3′ untranslated region associatedwith the genomic nucleic acid sequence. In some embodiments the nucleicacid molecule encoding a PIP-72 polypeptide is a non-genomic sequence

Sources of polynucleotides that encode PIP-72 polypeptides include butare not limited to SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO:7, SEQ ID NO: 9, SEQ ID NO: 11, SEQ ID NO: 13, SEQ ID NO: 17, SEQ ID NO:27 and SEQ ID NO: 31, SEQ ID NO: 949, SEQ ID NO: 950, SEQ ID NO: 955,SEQ ID NO: 956, SEQ ID NO: 957, SEQ ID NO: 958, SEQ ID NO: 961, SEQ IDNO: 962, SEQ ID NO: 963, SEQ ID NO: 965, SEQ ID NO: 966, SEQ ID NO: 967,and SEQ ID NO: 968. Examples of PIP-72 polypeptide sequences that can beused to obtain corresponding nucleotide encoding sequences include, butare not limited to, the PIP-72 polypeptide of sequence SEQ ID NO: 2, SEQID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 12, SEQID NO: 14, SEQ ID NO: 18, SEQ ID NO: 28 and SEQ ID NO: 32, SEQ ID NO:927, SEQ ID NO: 928, SEQ ID NO: 932, SEQ ID NO: 933, SEQ ID NO: 934, SEQID NO: 935, SEQ ID NO: 936, SEQ ID NO: 939, SEQ ID NO: 940, SEQ ID NO:941SEQ ID NO: 943, SEQ ID NO: 944, SEQ ID NO: 945 or SEQ ID NO:946.Nucleic acid molecules that are fragments of these nucleic acidsequences encoding PIP-72 polypeptides and a silencing element are alsoencompassed by the embodiments. “Fragment” as used herein refers to aportion of the nucleic acid sequence encoding a PIP-72 polypeptideand/or a silencing element. A fragment of a nucleic acid sequence mayencode a biologically active portion of a PIP-72 polypeptide or asilencing element or it may be a fragment that can be used as ahybridization probe or PCR primer using methods disclosed below. Nucleicacid molecules that are fragments of a nucleic acid sequence encoding aPIP-72 polypeptide or a silencing element comprise at least about 130,140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250 or 260,contiguous nucleotides or up to the number of nucleotides present in afull-length nucleic acid sequence encoding a PIP-72 polypeptide or asilencing element disclosed herein, depending upon the intended use.“Contiguous nucleotides” is used herein to refer to nucleotide residuesthat are immediately adjacent to one another. Fragments of the nucleicacid sequences of the embodiments will encode protein fragments orsilencing elements that retain the biological activity and, hence,retain insecticidal activity. “Retains activity” is used herein to referto a polypeptide or silencing element having at least about 10%, atleast about 30%, at least about 50%, at least about 70%, 80%, 90%, 95%or higher of the insecticidal activity of the full-length polypeptide ornucleic acid sequence. In one embodiment, the insecticidal activity isLepidoptera activity. In one embodiment, the insecticidal activity isagainst a Coleopteran species. In one embodiment, the insecticidalactivity is against a Diabrotica species. In one embodiment, theinsecticidal activity is against one or more insect pests of the cornrootworm complex: Western corn rootworm, Diabrotica virgifera virgifera;northern corn rootworm, D. barberi: Southern corn rootworm or spottedcucumber beetle; Diabrotica undecimpunctata howardi, and the Mexicancorn rootworm, D. virgifera zeae. In one embodiment, the insecticidalactivity is against Western corn rootworm, Diabrotica virgiferavirgifera.

In some embodiments the sequence identity is calculated using ClustalWalgorithm in the ALIGNX® module of the Vector NTI® Program Suite(Invitrogen Corporation, Carlsbad, Calif.) with all default parameters.In some embodiments the sequence identity is across the entire length ofpolypeptide calculated using ClustalW algorithm in the ALIGNX module ofthe Vector NTI Program Suite (Invitrogen Corporation, Carlsbad, Calif.)with all default parameters.

To determine the percent identity of two amino acid sequences or of twonucleic acid sequences, the sequences are aligned for optimal comparisonpurposes. The percent identity between the two sequences is a functionof the number of identical positions shared by the sequences (i.e.,percent identity=number of identical positions/total number of positions(e.g., overlapping positions)×100). In one embodiment, the two sequencesare the same length. In another embodiment, the comparison is across theentirety of the reference sequence (e.g., across the entirety of one ofSEQ ID NO: 1, SEQ ID NO: 2). The percent identity between two sequencescan be determined using techniques similar to those described below,with or without allowing gaps. In calculating percent identity,typically exact matches are counted.

The determination of percent identity between two sequences can beaccomplished using a mathematical algorithm. A non-limiting example of amathematical algorithm utilized for the comparison of two sequences isthe algorithm of Karlin and Altschul, (1990) Proc. Natl. Acad. Sci. USA87:2264, modified as in Karlin and Altschul, (1993) Proc. Natl. Acad.Sci. USA 90:5873-5877. Such an algorithm is incorporated into the BLASTNand BLASTX programs of Altschul, et al., (1990) J. Mol. Biol. 215:403.BLAST nucleotide searches can be performed with the BLASTN program,score=100, wordlength=12, to obtain nucleic acid sequences homologous topesticidal nucleic acid molecules of the embodiments. BLAST proteinsearches can be performed with the BLASTX program, score=50,wordlength=3, to obtain amino acid sequences homologous to pesticidalprotein molecules of the embodiments. To obtain gapped alignments forcomparison purposes, Gapped BLAST (in BLAST 2.0) can be utilized asdescribed in Altschul, et al., (1997) Nucleic Acids Res. 25:3389.Alternatively, PSI-Blast can be used to perform an iterated search thatdetects distant relationships between molecules. See, Altschul, et al.,(1997) supra. When utilizing BLAST, Gapped BLAST, and PSI-Blastprograms, the default parameters of the respective programs (e.g.,BLASTX and BLASTN) can be used. Alignment may also be performed manuallyby inspection.

Another non-limiting example of a mathematical algorithm utilized forthe comparison of sequences is the ClustalW algorithm (Higgins, et al.,(1994) Nucleic Acids Res. 22:4673-4680). ClustalW compares sequences andaligns the entirety of the amino acid or DNA sequence, and thus canprovide data about the sequence conservation of the entire amino acidsequence. The ClustalW algorithm is used in several commerciallyavailable DNA/amino acid analysis software packages, such as the ALIGNX®module of the Vector NTI® Program Suite (Invitrogen Corporation,Carlsbad, Calif.). After alignment of amino acid sequences withClustalW, the percent amino acid identity can be assessed. Anon-limiting example of a software program useful for analysis ofClustalW alignments is GENEDOC™ GENEDOC™ (Karl Nicholas) allowsassessment of amino acid (or DNA) similarity and identity betweenmultiple proteins. Another non-limiting example of a mathematicalalgorithm utilized for the comparison of sequences is the algorithm ofMyers and Miller, (1988) CABIOS 4:11-17. Such an algorithm isincorporated into the ALIGN program (version 2.0), which is part of theGCG Wisconsin Genetics Software Package, Version 10 (available fromAccelrys, Inc., 9685 Scranton Rd., San Diego, Calif., USA). Whenutilizing the ALIGN program for comparing amino acid sequences, a PAM120weight residue table, a gap length penalty of 12, and a gap penalty of 4can be used.

Another non-limiting example of a mathematical algorithm utilized forthe comparison of sequences is the algorithm of Needleman and Wunsch,(1970) J. Mol. Biol. 48(3):443-453, used GAP Version 10 software todetermine sequence identity or similarity using the following defaultparameters: % identity and % similarity for a nucleic acid sequenceusing GAP Weight of 50 and Length Weight of 3, and the nwsgapdna.cmpiiscoring matrix; % identity or % similarity for an amino acid sequenceusing GAP weight of 8 and length weight of 2, and the BLOSUM62 scoringprogram. Equivalent programs may also be used. “Equivalent program” isused herein to refer to any sequence comparison program that, for anytwo sequences in question, generates an alignment having identicalnucleotide residue matches and an identical percent sequence identitywhen compared to the corresponding alignment generated by GAP Version10.

The embodiments also encompass nucleic acid molecules encoding PIP-72polypeptide variants and a silencing element. “Variants” of the nucleicacid sequences disclosed herein include those sequences that differconservatively because of the degeneracy of the genetic code as well asthose that are sufficiently identical as discussed above. Naturallyoccurring allelic variants can be identified with the use of well-knownmolecular biology techniques, such as polymerase chain reaction (PCR)and hybridization techniques as outlined below. Variant nucleic acidsequences also include synthetically derived nucleic acid sequences thathave been generated, for example, by using site-directed mutagenesis butwhich still encode the PIP-72 polypeptides disclosed as discussed below.

Descriptions of a variety of diversity generating procedures forgenerating modified nucleic acid sequences, e.g., those coding forpolypeptides having pesticidal activity or fragments thereof, are foundin the following publications and the references cited therein: Soong,et al., (2000) Nat Genet 25(4):436-439; Stemmer, et al., (1999) TumorTargeting 4:1-4; Ness, et al., (1999) Nat Biotechnol 17:893-896; Chang,et al., (1999) Nat Biotechnol 17:793-797; Minshull and Stemmer, (1999)Curr Opin Chem Biol 3:284-290; Christians, et al., (1999) Nat Biotechnol17:259-264; Crameri, et al., (1998) Nature 391:288-291; Crameri, et al.,(1997) Nat Biotechnol 15:436-438; Zhang, et al., (1997) PNAS USA94:4504-4509; Patten, et al., (1997) Curr Opin Biotechnol 8:724-733;Crameri, et al., (1996) Nat Med 2:100-103; Crameri, et al., (1996) NatBiotechnol 14:315-319; Gates, et al., (1996) J Mol Biol 255:373-386;Stemmer, (1996) “Sexual PCR and Assembly PCR” In: The Encyclopedia ofMolecular Biology. VCH Publishers, New York. pp. 447-457; Crameri andStemmer, (1995) BioTechniques 18:194-195; Stemmer, et al., (1995) Gene,164:49-53; Stemmer, (1995) Science 270: 1510; Stemmer, (1995)Bio/Technology 13:549-553; Stemmer, (1994) Nature 370:389-391 andStemmer, (1994) PNAS USA 91:10747-10751.

Mutational methods of generating diversity include, for example,site-directed mutagenesis (Ling, et al., (1997) Anal Biochem254(2):157-178; Dale, et al., (1996) Methods Mol Biol 57:369-374; Smith,(1985) Ann Rev Genet 19:423-462; Botstein and Shortle, (1985) Science229:1193-1201; Carter, (1986) Biochem J 237:1-7 and Kunkel, (1987) “Theefficiency of oligonucleotide directed mutagenesis” in Nucleic Acids &Molecular Biology (Eckstein and Lilley, eds., Springer Verlag, Berlin));mutagenesis using uracil containing templates (Kunkel, (1985) PNAS USA82:488-492; Kunkel, et al., (1987) Methods Enzymol 154:367-382 and Bass,et al., (1988) Science 242:240-245); oligonucleotide-directedmutagenesis (Zoller and Smith, (1983) Methods Enzymol 100:468-500;Zoller and Smith, (1987) Methods Enzymol 154:329-350 (1987); Zoller andSmith, (1982) Nucleic Acids Res 10:6487-6500), phosphorothioate-modifiedDNA mutagenesis (Taylor, et al., (1985) Nucl Acids Res 13:8749-8764;Taylor, et al., (1985) Nucl Acids Res 13:8765-8787 (1985); Nakamaye andEckstein, (1986) Nucl Acids Res 14:9679-9698; Sayers, et al., (1988)Nucl Acids Res 16:791-802 and Sayers, et al., (1988) Nucl Acids Res16:803-814); mutagenesis using gapped duplex DNA (Kramer, et al., (1984)Nucl Acids Res 12:9441-9456; Kramer and Fritz, (1987) Methods Enzymol154:350-367; Kramer, et al., (1988) Nucl Acids Res 16:7207 and Fritz, etal., (1988) Nucl Acids Res 16:6987-6999).

Additional suitable methods include point mismatch repair (Kramer, etal., (1984) Cell 38:879-887), mutagenesis using repair-deficient hoststrains (Carter, et al., (1985) Nucl Acids Res 13:4431-4443 and Carter,(1987) Methods in Enzymol 154:382-403), deletion mutagenesis(Eghtedarzadeh and Henikoff, (1986) Nucl Acids Res 14:5115),restriction-selection and restriction-purification (Wells, et al.,(1986) Phil Trans R Soc Lond A 317:415-423), mutagenesis by total genesynthesis (Nambiar, et al., (1984) Science 223:1299-1301; Sakamar andKhorana, (1988) Nucl Acids Res 14:6361-6372; Wells, et al., (1985) Gene34:315-323 and Grundström, et al., (1985) Nucl Acids Res 13:3305-3316),double-strand break repair (Mandecki, (1986) PNAS USA, 83:7177-7181 andArnold, (1993) Curr Opin Biotech 4:450-455). Additional details on manyof the above methods can be found in Methods Enzymol Volume 154, whichalso describes useful controls for trouble-shooting problems withvarious mutagenesis methods.

Additional details regarding various diversity generating methods can befound in the following US Patents, PCT Publications and Applications andEPO publications: U.S. Pat. No. 5,723,323, U.S. Pat. No. 5,763,192, U.S.Pat. No. 5,814,476, U.S. Pat. No. 5,817,483, U.S. Pat. No. 5,824,514,U.S. Pat. No. 5,976,862, U.S. Pat. No. 5,605,793, U.S. Pat. No.5,811,238, U.S. Pat. No. 5,830,721, U.S. Pat. No. 5,834,252, U.S. Pat.No. 5,837,458, WO 1995/22625, WO 1996/33207, WO 1997/20078, WO1997/35966, WO 1999/41402, WO 1999/41383, WO 1999/41369, WO 1999/41368,EP 752008, EP 0932670, WO 1999/23107, WO 1999/21979, WO 1998/31837, WO1998/27230, WO 1998/27230, WO 2000/00632, WO 2000/09679, WO 1998/42832,WO 1999/29902, WO 1998/41653, WO 1998/41622, WO 1998/42727, WO2000/18906, WO 2000/04190, WO 2000/42561, WO 2000/42559, WO 2000/42560,WO 2001/23401 and PCT/US01/06775.

The nucleotide sequences of the embodiments can also be used to isolatecorresponding sequences from other organisms. In this manner, methodssuch as PCR, hybridization, and the like can be used to identify suchsequences based on their sequence homology to the sequences set forthherein. Sequences that are selected based on their sequence identity tothe entire sequences set forth herein or to fragments thereof areencompassed by the embodiments. Such sequences include sequences thatare orthologs of the disclosed sequences. The term “orthologs” refers togenes derived from a common ancestral gene and which are found indifferent species as a result of speciation. Genes found in differentspecies are considered orthologs when their nucleotide sequences and/ortheir encoded protein sequences share substantial identity as definedelsewhere herein. Functions of orthologs are often highly conservedamong species.

In a PCR approach, oligonucleotide primers can be designed for use inPCR reactions to amplify corresponding DNA sequences from cDNA orgenomic DNA extracted from any organism of interest. Methods fordesigning PCR primers and PCR cloning are generally known in the art andare disclosed in Sambrook, et al., (1989) Molecular Cloning: ALaboratory Manual (2d ed., Cold Spring Harbor Laboratory Press,Plainview, N.Y.), hereinafter “Sambrook”. See also, Innis, et al., eds.(1990) PCR Protocols: A Guide to Methods and Applications (AcademicPress, New York); Innis and Gelfand, eds. (1995) PCR Strategies(Academic Press, New York); and Innis and Gelfand, eds. (1999) PCRMethods Manual (Academic Press, New York). Known methods of PCR include,but are not limited to, methods using paired primers, nested primers,single specific primers, degenerate primers, gene-specific primers,vector-specific primers, partially-mismatched primers, and the like.

Alternatively, mass spectrometry based protein identification method canbe used to identify homologs of PIP-72 polypeptides using protocols inthe literatures (Scott Patterson, (1998), 10.22, 1-24, Current Protocolin Molecular Biology published by John Wiley & Son Inc.). Specifically,LC-MS/MS based protein identification method is used to associate the MSdata of given cell lysate or desired molecular weight enriched samples(excised from SDS-PAGE gel of relevant molecular weight bands to PIP-72)with sequence information of PIP-72 (e.g., SEQ ID NO: 2)) and itshomologs. Any match in peptide sequences indicates the potential ofhaving the homologs in the samples. Additional techniques (proteinpurification and molecular biology) can be used to isolate the proteinand identify the sequences of the homologs.

In hybridization methods, all or part of the pesticidal nucleic acidsequence can be used to screen cDNA or genomic libraries. Methods forconstruction of such cDNA and genomic libraries are generally known inthe art and are disclosed in Sambrook and Russell, (2001), supra. Theso-called hybridization probes may be genomic DNA fragments, cDNAfragments, RNA fragments or other oligonucleotides and may be labeledwith a detectable group such as 32P or any other detectable marker, suchas other radioisotopes, a fluorescent compound, an enzyme or an enzymeco-factor. Probes for hybridization can be made by labeling syntheticoligonucleotides based on the nucleic acid sequence disclosed herein.Degenerate primers designed on the basis of conserved nucleotides oramino acid residues in the nucleic acid sequence or encoded amino acidsequence can additionally be used. The probe typically comprises aregion of nucleic acid sequence that hybridizes under stringentconditions to at least about 12, at least about 25, at least about 50,75, 100, 125, 150, 175 or 200 consecutive nucleotides of nucleic acidsequence of the disclosure or a fragment or variant thereof. Methods forthe preparation of probes for hybridization are generally known in theart and are disclosed in Sambrook and Russell, (2001), supra, hereinincorporated by reference.

For example, an entire nucleic acid sequencedisclosed herein or one ormore portions thereof may be used as a probe capable of specificallyhybridizing to corresponding nucleic acid sequences encoding PIP-72polypeptide-like sequences and messenger RNAs. To achieve specifichybridization under a variety of conditions, such probes includesequences that are unique and are preferably at least about 10nucleotides in length or at least about 20 nucleotides in length. Suchprobes may be used to amplify corresponding pesticidal sequences from achosen organism by PCR. This technique may be used to isolate additionalcoding sequences from a desired organism or as a diagnostic assay todetermine the presence of coding sequences in an organism. Hybridizationtechniques include hybridization screening of plated DNA libraries(either plaques or colonies; see, for example, Sambrook, et al., (1989)Molecular Cloning: A Laboratory Manual (2d ed., Cold Spring HarborLaboratory Press, Cold Spring Harbor, N.Y.).

Hybridization of such sequences may be carried out under stringentconditions. “Stringent conditions” or “stringent hybridizationconditions” is used herein to refer to conditions under which a probewill hybridize to its target sequence to a detectably greater degreethan to other sequences (e.g., at least 2-fold over background).Stringent conditions are sequence-dependent and will be different indifferent circumstances. By controlling the stringency of thehybridization and/or washing conditions, target sequences that are 100%complementary to the probe can be identified (homologous probing).Alternatively, stringency conditions can be adjusted to allow somemismatching in sequences so that lower degrees of similarity aredetected (heterologous probing). Generally, a probe is less than about1000 nucleotides in length, preferably less than 500 nucleotides inlength.

Typically, stringent conditions will be those in which the saltconcentration is less than about 1.5 M Na ion, typically about 0.01 to1.0 M Na ion concentration (or other salts) at pH 7.0 to 8.3 and thetemperature is at least about 30° C. for short probes (e.g., 10 to 50nucleotides) and at least about 60° C. for long probes (e.g., greaterthan 50 nucleotides). Stringent conditions may also be achieved with theaddition of destabilizing agents such as formamide. Exemplary lowstringency conditions include hybridization with a buffer solution of 30to 35% formamide, 1 M NaCl, 1% SDS (sodium dodecyl sulphate) at 37° C.,and a wash in 1× to 2×SSC (20×SSC=3.0 M NaCl/0.3 M trisodium citrate) at50 to 55° C. Exemplary moderate stringency conditions includehybridization in 40 to 45% formamide, 1.0 M NaCl, 1% SDS at 37° C., anda wash in 0.5× to 1×SSC at 55 to 60° C. Exemplary high stringencyconditions include hybridization in 50% formamide, 1 M NaC., 1% SDS at37° C., and a wash in 0.1×SSC at 60 to 65° C. Optionally, wash buffersmay comprise about 0.1% to about 1% SDS. Duration of hybridization isgenerally less than about 24 hours, usually about 4 to about 12 hours.

Specificity is typically the function of post-hybridization washes, thecritical factors being the ionic strength and temperature of the finalwash solution. For DNA-DNA hybrids, the Tm can be approximated from theequation of Meinkoth and Wahl, (1984) Anal. Biochem. 138:267-284:Tm=81.5° C.+16.6 (log M)+0.41 (% GC)-0.61 (% form)-500/L; where M is themolarity of monovalent cations, % GC is the percentage of guanosine andcytosine nucleotides in the DNA, % form is the percentage of formamidein the hybridization solution, and L is the length of the hybrid in basepairs. The Tm is the temperature (under defined ionic strength and pH)at which 50% of a complementary target sequence hybridizes to aperfectly matched probe. Tm is reduced by about 1° C. for each 1% ofmismatching; thus, Tm, hybridization, and/or wash conditions can beadjusted to hybridize to sequences of the desired identity. For example,if sequences with ≧90% identity are sought, the Tm can be decreased 10°C. Generally, stringent conditions are selected to be about 5° C. lowerthan the thermal melting point (Tm) for the specific sequence and itscomplement at a defined ionic strength and pH. However, severelystringent conditions can utilize a hybridization and/or wash at 1, 2, 3or 4° C. lower than the thermal melting point (Tm); moderately stringentconditions can utilize a hybridization and/or wash at 6, 7, 8, 9 or 10°C. lower than the thermal melting point (Tm); low stringency conditionscan utilize a hybridization and/or wash at 11, 12, 13, 14, 15 or 20° C.lower than the thermal melting point (Tm). Using the equation,hybridization and wash compositions, and desired Tm, those of ordinaryskill will understand that variations in the stringency of hybridizationand/or wash solutions are inherently described. If the desired degree ofmismatching results in a Tm of less than 45° C. (aqueous solution) or32° C. (formamide solution), it is preferred to increase the SSCconcentration so that a higher temperature can be used. An extensiveguide to the hybridization of nucleic acids is found in Tijssen, (1993)Laboratory Techniques in Biochemistry and MolecularBiology-Hybridization with Nucleic Acid Probes, Part I, Chapter 2(Elsevier, New York); and Ausubel, et al., eds. (1995) Current Protocolsin Molecular Biology, Chapter 2 (Greene Publishing andWiley-Interscience, New York). See, Sambrook, et al., (1989) MolecularCloning: A Laboratory Manual (2d ed., Cold Spring Harbor LaboratoryPress, Cold Spring Harbor, N.Y.).

As used herein, the terms “protein,” “peptide molecule,” or“polypeptide” includes any molecule that comprises five or more aminoacids. It is well known in the art that protein, peptide or polypeptidemolecules may undergo modification, including post-translationalmodifications, such as, but not limited to, disulfide bond formation,glycosylation, phosphorylation or oligomerization. Thus, as used herein,the terms “protein,” “peptide molecule” or “polypeptide” includes anyprotein that is modified by any biological or non-biological process.The terms “amino acid” and “amino acids” refer to all naturallyoccurring L-amino acids.

A “recombinant protein” is used herein to refer to a protein that is nolonger in its natural environment, for example in vitro or in arecombinant bacterial or plant host cell. A PIP-72 polypeptide that issubstantially free of cellular material includes preparations of proteinhaving less than about 30%, 20%, 10% or 5% (by dry weight) ofnon-pesticidal protein (also referred to herein as a “contaminatingprotein”).

By “fragment” is intended a portion of the polynucleotide or a portionof the amino acid sequence and hence protein encoded thereby. Fragmentsof a polynucleotide may encode protein fragments that retain thebiological activity of the native protein. Fragments or “biologicallyactive portions” include polypeptide fragments comprising amino acidsequences sufficiently identical to a PIP-72 polypeptide and thatexhibit insecticidal activity. Alternatively, fragments of apolynucleotide that are useful as a silencing element do not need toencode fragment proteins that retain biological activity. Thus,fragments of a nucleotide sequence may range from at least about 10,about 15, about 16, about 17, about 18, about 19, nucleotides, about 20nucleotides, about 22 nucleotides, about 50 nucleotides, about 75nucleotides, about 100 nucleotides, 200 nucleotides, 300 nucleotides,400 nucleotides, 500 nucleotides, 600 nucleotides, 700 nucleotides andup to the full-length polynucleotide employed. Alternatively, fragmentsof a nucleotide sequence may range from 1-50, 25-75, 75-125, 50-100,125-175, 175-225, 100-150, 100-300, 150-200, 200-250, 225-275, 275-325,250-300, 325-375, 375-425, 300-350, 350-400, 425-475, 400-450, 475-525,450-500, 525-575, 575-625, 550-600, 625-675, 675-725, 600-650, 625-675,675-725, 650-700, 725-825, 825-875, 750-800, 875-925, 925-975, 850-900,925-975, 975-1025, 950-1000, 1000-1050, 1025-1075, 1075-1125, 1050-1100,1125-1175, 1100-1200, 1175-1225, 1225-1275, 1200-1300, 1325-1375,1375-1425, 1300-1400, 1425-1475, 1475-1525, 1400-1500, 1525-1575,1575-1625, 1625-1675, 1675-1725, 1725-1775, 1775-1825, 1825-1875,1875-1925, 1925-1975, 1975-2025, 2025-2075, 2075-2125, 2125-2175,2175-2225, 1500-1600, 1600-1700, 1700-1800, 1800-1900, 1900-2000 of thesequences disclosed herein. A biologically active portion of a PIP-72polypeptide can be a polypeptide that is, for example, 10, 25, 50, 55,60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77,78, 79, 80, 81, 82, 83, 84 or 85 amino acids in length. Suchbiologically active portions can be prepared by recombinant techniquesand evaluated for insecticidal activity. As used here, a fragmentcomprises at least 8 contiguous amino acids of a PIP-72 polypeptide.

In some embodiments exemplary PIP-72 polypeptides are set forth in SEQID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8, SEQ ID NO: 10, SEQID NO: 12, SEQ ID NO: 14; SEQ ID NO: 18, SEQ ID NO: 28, SEQ ID NO: 32,SEQ ID NO: 528, SEQ ID NO: 529, SEQ ID NO: 530, SEQ ID NO: 531, SEQ IDNO: 532, SEQ ID NO: 533, SEQ ID NO: 534, SEQ ID NO: 535, SEQ ID NO: 536,SEQ ID NO: 537, SEQ ID NO: 538, SEQ ID NO: 539, SEQ ID NO: 540, SEQ IDNO: 541, SEQ ID NO: 542, SEQ ID NO: 543, SEQ ID NO: 544, SEQ ID NO: 545,SEQ ID NO: 546, SEQ ID NO: 547, SEQ ID NO: 548, SEQ ID NO: 549, SEQ IDNO: 550, SEQ ID NO: 551, SEQ ID NO: 552, SEQ ID NO: 553, SEQ ID NO: 554,SEQ ID NO: 555, SEQ ID NO: 556, SEQ ID NO: 557, SEQ ID NO: 558, SEQ IDNO: 559, SEQ ID NO: 560, SEQ ID NO: 561, SEQ ID NO: 562, SEQ ID NO: 563,SEQ ID NO: 564, SEQ ID NO: 565, SEQ ID NO: 566, SEQ ID NO: 567, SEQ IDNO: 568, SEQ ID NO: 569, SEQ ID NO: 570, SEQ ID NO: 571, SEQ ID NO: 572,SEQ ID NO: 573, SEQ ID NO: 574, SEQ ID NO: 575, SEQ ID NO: 576, SEQ IDNO: 577, SEQ ID NO: 578, SEQ ID NO: 579, SEQ ID NO: 580, SEQ ID NO: 581,SEQ ID NO: 582, SEQ ID NO: 583, SEQ ID NO: 584, SEQ ID NO: 585, SEQ IDNO: 586, SEQ ID NO: 587, SEQ ID NO: 588, SEQ ID NO: 589, SEQ ID NO: 590,SEQ ID NO: 591, SEQ ID NO: 592, SEQ ID NO: 593, SEQ ID NO: 594, SEQ IDNO: 595, SEQ ID NO: 596, SEQ ID NO: 597, SEQ ID NO: 598, SEQ ID NO: 599,SEQ ID NO: 600, SEQ ID NO: 601, SEQ ID NO: 602, SEQ ID NO: 603, SEQ IDNO: 604, SEQ ID NO: 605, SEQ ID NO: 606, SEQ ID NO: 607, SEQ ID NO: 608,SEQ ID NO: 609, SEQ ID NO: 610, SEQ ID NO: 611, SEQ ID NO: 612, SEQ IDNO: 613, SEQ ID NO: 614, SEQ ID NO: 615, SEQ ID NO: 616, SEQ ID NO: 617,SEQ ID NO: 618, SEQ ID NO: 619, SEQ ID NO: 620, SEQ ID NO: 621, SEQ IDNO: 622, SEQ ID NO: 623, SEQ ID NO: 624, SEQ ID NO: 625, SEQ ID NO: 626,SEQ ID NO: 627, SEQ ID NO: 628, SEQ ID NO: 629, SEQ ID NO: 630, SEQ IDNO: 631, SEQ ID NO: 632, SEQ ID NO: 633, SEQ ID NO: 634, SEQ ID NO: 635,SEQ ID NO: 636, SEQ ID NO: 637, SEQ ID NO: 638, SEQ ID NO: 639, SEQ IDNO: 640, SEQ ID NO: 641, SEQ ID NO: 642, SEQ ID NO: 643, SEQ ID NO: 644,SEQ ID NO: 645, SEQ ID NO: 646, SEQ ID NO: 647, SEQ ID NO: 648, SEQ IDNO: 649, SEQ ID NO: 650, SEQ ID NO: 651, SEQ ID NO: 652, SEQ ID NO: 653,SEQ ID NO: 654, SEQ ID NO: 655, SEQ ID NO: 656, SEQ ID NO: 657, SEQ IDNO: 658, SEQ ID NO: 659, SEQ ID NO: 660, SEQ ID NO: 661, SEQ ID NO: 662,SEQ ID NO: 663, SEQ ID NO: 664, SEQ ID NO: 665, SEQ ID NO: 666, SEQ IDNO: 667, SEQ ID NO: 668, SEQ ID NO: 669, SEQ ID NO: 670, SEQ ID NO: 671,SEQ ID NO: 672, SEQ ID NO: 673, SEQ ID NO: 674, SEQ ID NO: 675, SEQ IDNO: 676, SEQ ID NO: 677, SEQ ID NO: 678, SEQ ID NO: 679, SEQ ID NO: 680,SEQ ID NO: 681, SEQ ID NO: 682, SEQ ID NO: 683, SEQ ID NO: 684, SEQ IDNO: 685, SEQ ID NO: 686, SEQ ID NO: 687, SEQ ID NO: 688, SEQ ID NO: 689,SEQ ID NO: 690, SEQ ID NO: 691, SEQ ID NO: 692, SEQ ID NO: 693, SEQ IDNO: 694, SEQ ID NO: 695, SEQ ID NO: 696, SEQ ID NO: 697, SEQ ID NO: 698,SEQ ID NO: 699, SEQ ID NO: 700, SEQ ID NO: 701, SEQ ID NO: 702, SEQ IDNO: 703, SEQ ID NO: 704, SEQ ID NO: 705, SEQ ID NO: 706, SEQ ID NO: 707,SEQ ID NO: 708, SEQ ID NO: 709, SEQ ID NO: 710, SEQ ID NO: 711, SEQ IDNO: 712, SEQ ID NO: 713, SEQ ID NO: 714, SEQ ID NO: 715, SEQ ID NO: 716,SEQ ID NO: 717, SEQ ID NO: 718, SEQ ID NO: 719, SEQ ID NO: 720, SEQ IDNO: 721, SEQ ID NO: 722, SEQ ID NO: 723, SEQ ID NO: 724, SEQ ID NO: 725,SEQ ID NO: 726, SEQ ID NO: 727, SEQ ID NO: 728, SEQ ID NO: 729, SEQ IDNO: 730, SEQ ID NO: 731, SEQ ID NO: 732, SEQ ID NO: 733, SEQ ID NO: 734,SEQ ID NO: 735, SEQ ID NO: 736, SEQ ID NO: 737, SEQ ID NO: 738, SEQ IDNO: 739, SEQ ID NO: 740, SEQ ID NO: 741, SEQ ID NO: 742, SEQ ID NO: 743,SEQ ID NO: 744, SEQ ID NO: 745, SEQ ID NO: 746, SEQ ID NO: 747, SEQ IDNO: 748, SEQ ID NO: 749, SEQ ID NO: 750, SEQ ID NO: 751, SEQ ID NO: 752,SEQ ID NO: 753, SEQ ID NO: 754, SEQ ID NO: 755, SEQ ID NO: 756, SEQ IDNO: 757, SEQ ID NO: 758, SEQ ID NO: 759, SEQ ID NO: 760, SEQ ID NO: 761,SEQ ID NO: 762, SEQ ID NO: 763, SEQ ID NO: 764, SEQ ID NO: 765, SEQ IDNO: 766, SEQ ID NO: 767, SEQ ID NO: 768, SEQ ID NO: 771, SEQ ID NO: 772,SEQ ID NO: 825, SEQ ID NO: 826, SEQ ID NO: 827, SEQ ID NO: 828, SEQ IDNO: 829, SEQ ID NO: 830, SEQ ID NO: 831, SEQ ID NO: 832, SEQ ID NO: 833,SEQ ID NO: 834, SEQ ID NO: 835, SEQ ID NO: 836, SEQ ID NO: 837, SEQ IDNO: 838, SEQ ID NO: 839, SEQ ID NO: 840, SEQ ID NO: 841, SEQ ID NO: 842,SEQ ID NO: 843, SEQ ID NO: 844, SEQ ID NO: 852, SEQ ID NO: 853, SEQ IDNO: 854, SEQ ID NO: 855, SEQ ID NO: 856, SEQ ID NO: 857, SEQ ID NO: 858,SEQ ID NO: 859, SEQ ID NO: 860, SEQ ID NO: 861, SEQ ID NO: 862, SEQ IDNO: 863, SEQ ID NO: 864, SEQ ID NO: 903, SEQ ID NO: 904, SEQ ID NO: 905,SEQ ID NO: 906, SEQ ID NO: 907, SEQ ID NO: 908, SEQ ID NO: 909, SEQ IDNO: 910, SEQ ID NO: 911, SEQ ID NO: 912, SEQ ID NO: 913, SEQ ID NO: 914,SEQ ID NO: 927, SEQ ID NO: 928, SEQ ID NO: 932, SEQ ID NO: 933, SEQ IDNO: 934, SEQ ID NO: 935, SEQ ID NO: 936, SEQ ID NO: 939, SEQ ID NO: 940,SEQ ID NO: 941, SEQ ID NO: 943, SEQ ID NO: 944, SEQ ID NO: 945 and SEQID NO: 946.

In some embodiments a PIP-72 polypeptide has a calculated molecularweight of between about 6 kDa and about 13 kDa between about 7 kDa andabout 12 kDa, between about 8 kDa and about 11 kDa, between about 9 kDaand about 10 kDa, about 8.75 kDa, about 9 kDa, about 9.25 kDa, about 9.5kDa, about 9.75 kDa, about 10 kDa, about 10.25 kDa, and about 10.5 kDa.As used herein, the term “about” used in the context of molecular weightof a PIP-72 polypeptide means ±0.25 kilodaltons.

In some embodiments the PIP-72 polypeptide has a modified physicalproperty. As used herein, the term “physical property” refers to anyparameter suitable for describing the physical-chemical characteristicsof a protein. As used herein, “physical property of interest” and“property of interest” are used interchangeably to refer to physicalproperties of proteins that are being investigated and/or modified.Examples of physical properties include, but are not limited to netsurface charge and charge distribution on the protein surface, nethydrophobicity and hydrophobic residue distribution on the proteinsurface, surface charge density, surface hydrophobicity density, totalcount of surface ionizable groups, surface tension, protein size and itsdistribution in solution, melting temperature, heat capacity, and secondvirial coefficient. Examples of physical properties also include, butare not limited to solubility, folding, stability, and digestibility. Insome embodiments the PIP-72 polypeptide has increased digestibility ofproteolytic fragments in an insect gut. Models for digestion bysimulated gastric fluids are known to one skilled in the art (Fuchs, R.L. and J. D. Astwood. Food Technology 50: 83-88, 1996; Astwood, J. D.,et al Nature Biotechnology 14: 1269-1273, 1996; Fu T J et al J. AgricFood Chem. 50: 7154-7160, 2002).

“Variants” is intended to mean substantially similar sequences. Forpolynucleotides, a variant comprises a deletion and/or addition of oneor more nucleotides at one or more internal sites within the nativepolynucleotide and/or a substitution of one or more nucleotides at oneor more sites in the native polynucleotide. A variant of apolynucleotide that is useful as a silencing element will retain theability to reduce expression of the target polynucleotide and, in someembodiments, thereby control a plant insect pest of interest. As usedherein, a “native” polynucleotide or polypeptide comprises a naturallyoccurring nucleotide sequence or amino acid sequence, respectively. Forpolynucleotides, conservative variants include those sequences that,because of the degeneracy of the genetic code, encode the amino acidsequence of one of the disclosed polypeptides. Variant polynucleotidesalso include synthetically derived polynucleotide, such as thosegenerated, for example, by using site-directed mutagenesis, but continueto retain the desired activity. Generally, variants of a particulardisclosed polynucleotide (i.e., a silencing element) will have at leastabout 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%,93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to thatparticular polynucleotide as determined by sequence alignment programsand parameters described elsewhere herein.

Variants of a particular disclosed polynucleotide (i.e., the referencepolynucleotide) can also be evaluated by comparison of the percentsequence identity between the polypeptide encoded by a variantpolynucleotide and the polypeptide encoded by the referencepolynucleotide. Percent sequence identity between any two polypeptidescan be calculated using sequence alignment programs and parametersdescribed elsewhere herein. Where any given pair of disclosedpolynucleotides employed is evaluated by comparison of the percentsequence identity shared by the two polypeptides they encode, thepercent sequence identity between the two encoded polypeptides is atleast about 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%,92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity.

In some embodiments variants include polypeptides that differ in aminoacid sequence due to mutagenesis. Variant proteins encompassed by thedisclosure are biologically active, that is they continue to possess thedesired biological activity (i.e. pesticidal activity) of the nativeprotein. In some embodiment the variant will have at least about 10%, atleast about 30%, at least about 50%, at least about 70%, at least about80% or more of the insecticidal activity of the native protein. In someembodiments, the variants may have improved activity over the nativeprotein.

Bacterial genes quite often possess multiple methionine initiationcodons in proximity to the start of the open reading frame. Often,translation initiation at one or more of these start codons will lead togeneration of a functional protein. These start codons can include ATGcodons. However, bacteria such as Bacillus sp. also recognize the codonGTG as a start codon, and proteins that initiate translation at GTGcodons contain a methionine at the first amino acid. On rare occasions,translation in bacterial systems can initiate at a TTG codon, though inthis event the TTG encodes a methionine. Furthermore, it is not oftendetermined a priori which of these codons are used naturally in thebacterium. Thus, it is understood that use of one of the alternatemethionine codons may also lead to generation of pesticidal proteins.These pesticidal proteins are encompassed in the present disclosure andmay be used in the methods of the present disclosure. It will beunderstood that, when expressed in plants, it will be necessary to alterthe alternate start codon to ATG for proper translation.

In another aspect the PIP-72 polypeptide may be expressed as a precursorprotein with an intervening sequence that catalyzes multi-step, posttranslational protein splicing. Protein splicing involves the excisionof an intervening sequence from a polypeptide with the concomitantjoining of the flanking sequences to yield a new polypeptide (Chong, etal., (1996) J. Biol. Chem., 271:22159-22168). This intervening sequenceor protein splicing element, referred to as inteins, which catalyzetheir own excision through three coordinated reactions at the N-terminaland C-terminal splice junctions: an acyl rearrangement of the N-terminalcysteine or serine; a transesterfication reaction between the twotermini to form a branched ester or thioester intermediate and peptidebond cleavage coupled to cyclization of the intein C-terminal asparagineto free the intein (Evans, et al., (2000) J. Biol. Chem., 275:9091-9094.The elucidation of the mechanism of protein splicing has led to a numberof intein-based applications (Comb, et al., U.S. Pat. No. 5,496,714;Comb, et al., U.S. Pat. No. 5,834,247; Camarero and Muir, (1999) J.Amer. Chem. Soc. 121:5597-5598; Chong, et al., (1997) Gene 192:271-281,Chong, et al., (1998) Nucleic Acids Res. 26:5109-5115; Chong, et al.,(1998) J. Biol. Chem. 273:10567-10577; Cotton, et al., (1999) J. Am.Chem. Soc. 121:1100-1101; Evans, et al., (1999) J. Biol. Chem.274:18359-18363; Evans, et al., (1999) J. Biol. Chem. 274:3923-3926;Evans, et al., (1998) Protein Sci. 7:2256-2264; Evans, et al., (2000) J.Biol. Chem. 275:9091-9094; Iwai and Pluckthun, (1999) FEBS Lett.459:166-172; Mathys, et al., (1999) Gene 231:1-13; Mills, et al., (1998)Proc. Natl. Acad. Sci. USA 95:3543-3548; Muir, et al., (1998) Proc.Natl. Acad. Sci. USA 95:6705-6710; Otomo, et al., (1999) Biochemistry38:16040-16044; Otomo, et al., (1999) J. Biolmol. NMR 14:105-114; Scott,et al., (1999) Proc. Natl. Acad. Sci. USA 96:13638-13643; Severinov andMuir, (1998) J. Biol. Chem. 273:16205-16209; Shingledecker, et al.,(1998) Gene 207:187-195; Southworth, et al., (1998) EMBO J. 17:918-926;Southworth, et al., (1999) Biotechniques 27:110-120; Wood, et al.,(1999) Nat. Biotechnol. 17:889-892; Wu, et al., (1998a) Proc. Natl.Acad. Sci. USA 95:9226-9231; Wu, et al., (1998b) Biochim Biophys Acta1387:422-432; Xu, et al., (1999) Proc. Natl. Acad. Sci. USA 96:388-393;Yamazaki, et al., (1998) J. Am. Chem. Soc., 120:5591-5592). For theapplication of inteins in plant transgenes, see, Yang, et al.,(Transgene Res 15:583-593 (2006)) and Evans, et al., (Annu. Rev. PlantBiol. 56:375-392 (2005)).

In another aspect the PIP-72 polypeptide may be encoded by two separategenes where the intein of the precursor protein comes from the twogenes, referred to as a split-intein, and the two portions of theprecursor are joined by a peptide bond formation. This peptide bondformation is accomplished by intein-mediated trans-splicing. For thispurpose, a first and a second expression cassette comprising the twoseparate genes further code for inteins capable of mediating proteintrans-splicing. By trans-splicing, the proteins and polypeptides encodedby the first and second fragments may be linked by peptide bondformation. Trans-splicing inteins may be selected from the nucleolar andorganellar genomes of different organisms including eukaryotes,archaebacteria and eubacteria. Inteins that may be used for are listedat neb.com/neb/inteins.html, which can be accessed on the world-wide webusing the “www” prefix). The nucleotide sequence coding for an inteinmay be split into a 5′ and a 3′ part that code for the 5′ and the 3′part of the intein, respectively. Sequence portions not necessary forintein splicing (e.g. homing endonuclease domain) may be deleted. Theintein coding sequence is split such that the 5′ and the 3′ parts arecapable of trans-splicing. For selecting a suitable splitting site ofthe intein coding sequence, the considerations published by Southworth,et al., (1998) EMBO J. 17:918-926 may be followed. In constructing thefirst and the second expression cassette, the 5′ intein coding sequenceis linked to the 3′ end of the first fragment coding for the N-terminalpart of the PIP-72 polypeptide and the 3′ intein coding sequence islinked to the 5′ end of the second fragment coding for the C-terminalpart of the PIP-72 polypeptide.

In general, the trans-splicing partners can be designed using any splitintein, including any naturally-occurring or artificially-split splitintein. Several naturally-occurring split inteins are known, forexample: the split intein of the DnaE gene of Synechocystis sp. PCC6803(see, Wu, et al., (1998) Proc Natl Acad Sci USA. 95(16):9226-31 andEvans, et al., (2000) J Biol Chem. 275(13):9091-4 and of the DnaE genefrom Nostoc punctiforme (see, Iwai, et al., (2006) FEBS Lett.580(7):1853-8). Non-split inteins have been artificially split in thelaboratory to create new split inteins, for example: the artificiallysplit Ssp DnaB intein (see, Wu, et al., (1998) Biochim Biophys Acta.1387:422-32) and split Sce VMA intein (see, Brenzel, et al., (2006)Biochemistry. 45(6):1571-8) and an artificially split fungal mini-intein(see, Elleuche, et al., (2007) Biochem Biophys Res Commun.355(3):830-4). There are also intein databases available that catalogueknown inteins (see for example the online-database available at:bioinformatics.weizmann.ac.il/{tilde over ()}pietro/inteins/Inteinstable.html, which can be accessed on theworld-wide web using the “www” prefix).

Naturally-occurring non-split inteins may have endonuclease or otherenzymatic activities that can typically be removed when designing anartificially-split split intein. Such mini-inteins or minimized splitinteins are well known in the art and are typically less than 200 aminoacid residues long (see, Wu, et al., (1998) Biochim Biophys Acta.1387:422-32). Suitable split inteins may have other purificationenabling polypeptide elements added to their structure, provided thatsuch elements do not inhibit the splicing of the split intein or areadded in a manner that allows them to be removed prior to splicing.Protein splicing has been reported using proteins that comprisebacterial intein-like (BIL) domains (see, Amitai, et al., (2003) MolMicrobiol. 47:61-73) and hedgehog (Hog) auto-processing domains (thelatter is combined with inteins when referred to as the Hog/inteinsuperfamily or HINT family (see, Dassa, et al., (2004) J Biol Chem.279:32001-7) and domains such as these may also be used to prepareartificially-split inteins. In particular, non-splicing members of suchfamilies may be modified by molecular biology methodologies to introduceor restore splicing activity in such related species. Recent studiesdemonstrate that splicing can be observed when a N-terminal split inteincomponent is allowed to react with a C-terminal split intein componentnot found in nature to be its “partner”; for example, splicing has beenobserved utilizing partners that have as little as 30 to 50% homologywith the “natural” splicing partner (see, Dassa, et al., (2007)Biochemistry. 46(1):322-30). Other such mixtures of disparate splitintein partners have been shown to be unreactive one with another (see,Brenzel, et al., (2006) Biochemistry. 45(6):1571-8). However, it iswithin the ability of a person skilled in the relevant art to determinewhether a particular pair of polypeptides is able to associate with eachother to provide a functional intein, using routine methods and withoutthe exercise of inventive skill.

The development of recombinant DNA methods has made it possible to studythe effects of sequence transposition on protein folding, structure andfunction. The approach used in creating new sequences resembles that ofnaturally occurring pairs of proteins that are related by linearreorganization of their amino acid sequences (Cunningham, et al., (1979)Proc. Natl. Acad. Sci. U.S.A. 76:3218-3222; Teather and Erfle, (1990) J.Bacteriol. 172:3837-3841; Schimming, et al., (1992) Eur. J. Biochem.204:13-19; Yamiuchi and Minamikawa, (1991) FEBS Lett. 260:127-130;MacGregor, et al., (1996) FEBS Lett. 378:263-266). The first in vitroapplication of this type of rearrangement to proteins was described byGoldenberg and Creighton (J. Mol. Biol. 165:407-413, 1983). In creatinga circular permuted variant a new N-terminus is selected at an internalsite (breakpoint) of the original sequence, the new sequence having thesame order of amino acids as the original from the breakpoint until itreaches an amino acid that is at or near the original C-terminus. Atthis point the new sequence is joined, either directly or through anadditional portion of sequence (linker), to an amino acid that is at ornear the original N-terminus and the new sequence continues with thesame sequence as the original until it reaches a point that is at ornear the amino acid that was N-terminal to the breakpoint site of theoriginal sequence, this residue forming the new C-terminus of the chain.The length of the amino acid sequence of the linker can be selectedempirically or with guidance from structural information or by using acombination of the two approaches. When no structural information isavailable, a small series of linkers can be prepared for testing using adesign whose length is varied in order to span a range from 0 to 50 Åand whose sequence is chosen in order to be consistent with surfaceexposure (hydrophilicity, Hopp and Woods, (1983) Mol. lmmunol.20:483-489; Kyte and Doolittle, (1982) J. Mol. Biol. 157:105-132;solvent exposed surface area, Lee and Richards, (1971) J. Mol. Biol.55:379-400) and the ability to adopt the necessary conformation withoutderanging the configuration of the pesticidal polypeptide(conformationally flexible; Karplus and Schulz, (1985)Naturwissenschaften 72:212-213). Assuming an average of translation of2.0 to 3.8 Å per residue, this would mean the length to test would bebetween 0 to 30 residues, with 0 to 15 residues being the preferredrange. Exemplary of such an empirical series would be to constructlinkers using a cassette sequence such as Gly-Gly-Gly-Ser repeated ntimes, where n is 1, 2, 3 or 4. Those skilled in the art will recognizethat there are many such sequences that vary in length or compositionthat can serve as linkers with the primary consideration being that theybe neither excessively long nor short (cf., Sandhu, (1992) Critical Rev.Biotech. 12:437-462); if they are too long, entropy effects will likelydestabilize the three-dimensional fold, and may also make foldingkinetically impractical, and if they are too short, they will likelydestabilize the molecule because of torsional or steric strain. Thoseskilled in the analysis of protein structural information will recognizethat using the distance between the chain ends, defined as the distancebetween the c-alpha carbons, can be used to define the length of thesequence to be used or at least to limit the number of possibilitiesthat must be tested in an empirical selection of linkers. They will alsorecognize that it is sometimes the case that the positions of the endsof the polypeptide chain are ill-defined in structural models derivedfrom x-ray diffraction or nuclear magnetic resonance spectroscopy data,and that when true, this situation will therefore need to be taken intoaccount in order to properly estimate the length of the linker required.From those residues whose positions are well defined are selected tworesidues that are close in sequence to the chain ends, and the distancebetween their c-alpha carbons is used to calculate an approximate lengthfor a linker between them. Using the calculated length as a guide,linkers with a range of number of residues (calculated using 2 to 3.8 Åper residue) are then selected. These linkers may be composed of theoriginal sequence, shortened or lengthened as necessary, and whenlengthened the additional residues may be chosen to be flexible andhydrophilic as described above; or optionally the original sequence maybe substituted for using a series of linkers, one example being theGly-Gly-Gly-Ser cassette approach mentioned above; or optionally acombination of the original sequence and new sequence having theappropriate total length may be used. Sequences of pesticidalpolypeptides capable of folding to biologically active states can beprepared by appropriate selection of the beginning (amino terminus) andending (carboxyl terminus) positions from within the originalpolypeptide chain while using the linker sequence as described above.Amino and carboxyl termini are selected from within a common stretch ofsequence, referred to as a breakpoint region, using the guidelinesdescribed below. A novel amino acid sequence is thus generated byselecting amino and carboxyl termini from within the same breakpointregion. In many cases the selection of the new termini will be such thatthe original position of the carboxyl terminus immediately preceded thatof the amino terminus. However, those skilled in the art will recognizethat selections of termini anywhere within the region may function, andthat these will effectively lead to either deletions or additions to theamino or carboxyl portions of the new sequence. It is a central tenet ofmolecular biology that the primary amino acid sequence of a proteindictates folding to the three-dimensional structure necessary forexpression of its biological function. Methods are known to thoseskilled in the art to obtain and interpret three-dimensional structuralinformation using x-ray diffraction of single protein Crystals ornuclear magnetic resonance spectroscopy of protein solutions. Examplesof structural information that are relevant to the identification ofbreakpoint regions include the location and type of protein secondarystructure (alpha and 3-10 helices, parallel and anti-parallel betasheets, chain reversals and turns, and loops; Kabsch and Sander, (1983)Biopolymers 22:2577-2637; the degree of solvent exposure of amino acidresidues, the extent and type of interactions of residues with oneanother (Chothia, (1984) Ann. Rev. Biochem. 53:537-572) and the staticand dynamic distribution of conformations along the polypeptide chain(Alber and Mathews, (1987) Methods Enzymol. 154:511-533). In some casesadditional information is known about solvent exposure of residues; oneexample is a site of post-translational attachment of carbohydrate whichis necessarily on the surface of the protein. When experimentalstructural information is not available or is not feasible to obtain,methods are also available to analyze the primary amino acid sequence inorder to make predictions of protein tertiary and secondary structure,solvent accessibility and the occurrence of turns and loops. Biochemicalmethods are also sometimes applicable for empirically determiningsurface exposure when direct structural methods are not feasible; forexample, using the identification of sites of chain scission followinglimited proteolysis in order to infer surface exposure (Gentile andSalvatore, (1993) Eur. J. Biochem. 218:603-621). Thus using either theexperimentally derived structural information or predictive methods(e.g., Srinivisan and Rose, (1995) Proteins: Struct., Funct. & Genetics22:81-99) the parental amino acid sequence is inspected to classifyregions according to whether or not they are integral to the maintenanceof secondary and tertiary structure. The occurrence of sequences withinregions that are known to be involved in periodic secondary structure(alpha and 3-10 helices, parallel and anti-parallel beta sheets) areregions that should be avoided. Similarly, regions of amino acidsequence that are observed or predicted to have a low degree of solventexposure are more likely to be part of the so-called hydrophobic core ofthe protein and should also be avoided for selection of amino andcarboxyl termini. In contrast, those regions that are known or predictedto be in surface turns or loops, and especially those regions that areknown not to be required for biological activity, are the preferredsites for location of the extremes of the polypeptide chain. Continuousstretches of amino acid sequence that are preferred based on the abovecriteria are referred to as a breakpoint region. Polynucleotidesencoding circular permuted PIP-72 polypeptides with newN-terminus/C-terminus which contain a linker region separating theoriginal C-terminus and N-terminus can be made essentially following themethod described in Mullins, et al., (1994) J. Am. Chem. Soc.116:5529-5533. Multiple steps of polymerase chain reaction (PCR)amplifications are used to rearrange the DNA sequence encoding theprimary amino acid sequence of the protein. Polynucleotides encodingcircular permuted PIP-72 polypeptides with new N-terminus/C-terminuswhich contain a linker region separating the original C-terminus andN-terminus can be made based on the tandem-duplication method describedin Horlick, et al., (1992) Protein Eng. 5:427-431. Polymerase chainreaction (PCR) amplification of the new N-terminus/C-terminus genes isperformed using a tandemly duplicated template DNA.

Methods for design and construction of fusion proteins (andpolynucleotides encoding same) are known to those of skill in the art.Polynucleotides encoding a PIP-72 polypeptide may be fused to signalsequences which will direct the localization of the PIP-72 polypeptideto particular compartments of a prokaryotic or eukaryotic cell and/ordirect the secretion of the PIP-72 polypeptide of the embodiments from aprokaryotic or eukaryotic cell. For example, in E. coli, one may wish todirect the expression of the protein to the periplasmic space. Examplesof signal sequences or proteins (or fragments thereof) to which thePIP-72 polypeptide may be fused in order to direct the expression of thepolypeptide to the periplasmic space of bacteria include, but are notlimited to, the pelB signal sequence, the maltose binding protein (MBP)signal sequence, MBP, the ompA signal sequence, the signal sequence ofthe periplasmic E. coli heat-labile enterotoxin B-subunit and the signalsequence of alkaline phosphatase. Several vectors are commerciallyavailable for the construction of fusion proteins which will direct thelocalization of a protein, such as the pMAL series of vectors(particularly the pMAL-p series) available from New England Biolabs®(240 County Road, Ipswich, Mass. 01938-2723). In a specific embodiment,the PIP-72 polypeptide may be fused to the pelB pectate lyase signalsequence to increase the efficiency of expression and purification ofsuch polypeptides in Gram-negative bacteria (see, U.S. Pat. Nos.5,576,195 and 5,846,818). Plant plastid transit peptide/polypeptidefusions are well known in the art (see, U.S. Pat. No. 7,193,133).Apoplast transit peptides such as rice or barley alpha-amylase secretionsignal are also well known in the art. The plastid transit peptide isgenerally fused N-terminal to the polypeptide to be targeted (e.g., thefusion partner). In one embodiment, the fusion protein consistsessentially of the plastid transit peptide and the PIP-72 polypeptide tobe targeted. In another embodiment, the fusion protein comprises theplastid transit peptide and the polypeptide to be targeted. In suchembodiments, the plastid transit peptide is preferably at the N-terminusof the fusion protein. However, additional amino acid residues may beN-terminal to the plastid transit peptide providing that the fusionprotein is at least partially targeted to a plastid. In a specificembodiment, the plastid transit peptide is in the N-terminal half,N-terminal third or N-terminal quarter of the fusion protein. Most orall of the plastid transit peptide is generally cleaved from the fusionprotein upon insertion into the plastid. The position of cleavage mayvary slightly between plant species, at different plant developmentalstages, as a result of specific intercellular conditions or theparticular combination of transit peptide/fusion partner used. In oneembodiment, the plastid transit peptide cleavage is homogenous such thatthe cleavage site is identical in a population of fusion proteins. Inanother embodiment, the plastid transit peptide is not homogenous, suchthat the cleavage site varies by 1-10 amino acids in a population offusion proteins. The plastid transit peptide can be recombinantly fusedto a second protein in one of several ways. For example, a restrictionendonuclease recognition site can be introduced into the nucleotidesequence of the transit peptide at a position corresponding to itsC-terminal end and the same or a compatible site can be engineered intothe nucleotide sequence of the protein to be targeted at its N-terminalend. Care must be taken in designing these sites to ensure that thecoding sequences of the transit peptide and the second protein are kept“in frame” to allow the synthesis of the desired fusion protein. In somecases, it may be preferable to remove the initiator methionine codon ofthe second protein when the new restriction site is introduced. Theintroduction of restriction endonuclease recognition sites on bothparent molecules and their subsequent joining through recombinant DNAtechniques may result in the addition of one or more extra amino acidsbetween the transit peptide and the second protein. This generally doesnot affect targeting activity as long as the transit peptide cleavagesite remains accessible and the function of the second protein is notaltered by the addition of these extra amino acids at its N-terminus.Alternatively, one skilled in the art can create a precise cleavage sitebetween the transit peptide and the second protein (with or without itsinitiator methionine) using gene synthesis (Stemmer, et al., (1995) Gene164:49-53) or similar methods. In addition, the transit peptide fusioncan intentionally include amino acids downstream of the cleavage site.The amino acids at the N-terminus of the mature protein can affect theability of the transit peptide to target proteins to plastids and/or theefficiency of cleavage following protein import. This may be dependenton the protein to be targeted. See, e.g., Comai, et al., (1988) J. Biol.Chem. 263(29):15104-9.

In some embodiments fusion proteins are provide comprising a PIP-72polypeptide, and an insecticidal polypeptide joined by an amino acidlinker.

It is recognized that DNA sequences may be altered by various methods,and that these alterations may result in DNA sequences encoding proteinswith amino acid sequences different than that encoded by the wild-type(or native) pesticidal protein. In some embodiments a PIP-72 polypeptidemay be altered in various ways including amino acid substitutions,deletions, truncations and insertions of one or more amino acids,including up to 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,36, 37, 38, 39, 40, 41, 42, 43, 44, 45 or more amino acid substitutions,deletions and/or insertions or combinations thereof compared to thepolypeptide sequences disclosed herein.

Methods for such manipulations are generally known in the art. Forexample, amino acid sequence variants of a PIP-72 polypeptide can beprepared by mutations in the DNA. This may also be accomplished by oneof several forms of mutagenesis and/or in directed evolution. In someaspects, the changes encoded in the amino acid sequence will notsubstantially affect the function of the protein. Such variants willpossess the desired pesticidal activity. However, it is understood thatthe ability of a PIP-72 polypeptide to confer pesticidal activity may beimproved by the use of such techniques upon the compositions of thisdisclosure.

For example, conservative amino acid substitutions may be made at one ormore, predicted, nonessential amino acid residues. A “nonessential”amino acid residue is a residue that can be altered from the wild-typesequence of a PIP-72 polypeptide without altering the biologicalactivity. A “conservative amino acid substitution” is one in which theamino acid residue is replaced with an amino acid residue having asimilar side chain. Families of amino acid residues having similar sidechains have been defined in the art. These families include: amino acidswith basic side chains (e.g., lysine, arginine, histidine); acidic sidechains (e.g., aspartic acid, glutamic acid); polar, negatively chargedresidues and their amides (e.g., aspartic acid, asparagine, glutamic,acid, glutamine; uncharged polar side chains (e.g., glycine, asparagine,glutamine, serine, threonine, tyrosine, cysteine); small aliphatic,nonpolar or slightly polar residues (e.g., Alanine, serine, threonine,proline, glycine); nonpolar side chains (e.g., alanine, valine, leucine,isoleucine, proline, phenylalanine, methionine, tryptophan); largealiphatic, nonpolar residues (e.g., methionine, leucine, isoleucine,valine, cysteine); beta-branched side chains (e.g., threonine, valine,isoleucine); aromatic side chains (e.g., tyrosine, phenylalanine,tryptophan, histidine); large aromatic side chains (e.g., tyrosine,phenylalanine, tryptophan).

Amino acid substitutions may be made in nonconserved regions that retainfunction. In general, such substitutions would not be made for conservedamino acid residues or for amino acid residues residing within aconserved motif, where such residues are essential for protein activity.Examples of residues that are conserved and that may be essential forprotein activity include, for example, residues that are identicalbetween all proteins contained in an alignment of similar or relatedtoxins to the sequences of the embodiments (e.g., residues that areidentical in an alignment of homologs). Examples of residues that areconserved but that may allow conservative amino acid substitutions andstill retain activity include, for example, residues that have onlyconservative substitutions between all proteins contained in analignment of similar or related toxins to the sequences of theembodiments (e.g., residues that have only conservative substitutionsbetween all proteins contained in the alignment of the homologs).However, one of skill in the art would understand that functionalvariants may have minor conserved or nonconserved alterations in theconserved residues. Guidance as to appropriate amino acid substitutionsthat do not affect biological activity of the protein of interest may befound in the model of Dayhoff, et al., (1978) Atlas of Protein Sequenceand Structure (Natl. Biomed. Res. Found., Washington, D.C.), hereinincorporated by reference.

In making such changes, the hydropathic index of amino acids may beconsidered. The importance of the hydropathic amino acid index inconferring interactive biologic function on a protein is generallyunderstood in the art (Kyte and Doolittle, (1982) J Mol Biol.157(1):105-32). It is accepted that the relative hydropathic characterof the amino acid contributes to the secondary structure of theresultant protein, which in turn defines the interaction of the proteinwith other molecules, for example, enzymes, substrates, receptors, DNA,antibodies, antigens, and the like.

It is known in the art that certain amino acids may be substituted byother amino acids having a similar hydropathic index or score and stillresult in a protein with similar biological activity, i.e., still obtaina biological functionally equivalent protein. Each amino acid has beenassigned a hydropathic index on the basis of its hydrophobicity andcharge characteristics (Kyte and Doolittle, ibid). These are: isoleucine(+4.5); valine (+4.2); leucine (+3.8); phenylalanine (+2.8);cysteine/cysteine (+2.5); methionine (+1.9); alanine (+1.8); glycine(−0.4); threonine (−0.7); serine (−0.8); tryptophan (−0.9); tyrosine(−1.3); proline (−1.6); histidine (−3.2); glutamate (−3.5); glutamine(−3.5); aspartate (−3.5); asparagine (−3.5); lysine (−3.9) and arginine(−4.5). In making such changes, the substitution of amino acids whosehydropathic indices are within +2 is preferred, those which are within+1 are particularly preferred, and those within +0.5 are even moreparticularly preferred.

It is also understood in the art that the substitution of like aminoacids can be made effectively on the basis of hydrophilicity. U.S. Pat.No. 4,554,101, states that the greatest local average hydrophilicity ofa protein, as governed by the hydrophilicity of its adjacent aminoacids, correlates with a biological property of the protein.

As detailed in U.S. Pat. No. 4,554,101, the following hydrophilicityvalues have been assigned to amino acid residues: arginine (+3.0);lysine (+3.0); aspartate (+3.0.+0.1); glutamate (+3.0.+0.1); serine(+0.3); asparagine (+0.2); glutamine (+0.2); glycine (0); threonine(−0.4); proline (−0.5.+0.1); alanine (−0.5); histidine (−0.5); cysteine(−1.0); methionine (−1.3); valine (−1.5); leucine (−1.8); isoleucine(−1.8); tyrosine (−2.3); phenylalanine (−2.5); tryptophan (−3.4).

Alternatively, alterations may be made to the protein sequence of manyproteins at the amino or carboxy terminus without substantiallyaffecting activity. This can include insertions, deletions oralterations introduced by modern molecular methods, such as PCR,including PCR amplifications that alter or extend the protein codingsequence by virtue of inclusion of amino acid encoding sequences in theoligonucleotides utilized in the PCR amplification. Alternatively, theprotein sequences added can include entire protein-coding sequences,such as those used commonly in the art to generate protein fusions. Suchfusion proteins are often used to (1) increase expression of a proteinof interest (2) introduce a binding domain, enzymatic activity orepitope to facilitate either protein purification, protein detection orother experimental uses known in the art (3) target secretion ortranslation of a protein to a subcellular organelle, such as theperiplasmic space of Gram-negative bacteria, mitochondria orchloroplasts of plants or the endoplasmic reticulum of eukaryotic cells,the latter of which often results in glycosylation of the protein.

Variant nucleotide and amino acid sequences of the disclosure alsoencompass sequences derived from mutagenic and recombinogenic proceduressuch as DNA shuffling. With such a procedure, one or more differentPIP-72 polypeptide coding regions can be used to create a new PIP-72polypeptide possessing the desired properties. In this manner, librariesof recombinant polynucleotides are generated from a population ofrelated sequence polynucleotides comprising sequence regions that havesubstantial sequence identity and can be homologously recombined invitro or in vivo. For example, using this approach, sequence motifsencoding a domain of interest may be shuffled between a pesticidal geneand other known pesticidal genes to obtain a new gene coding for aprotein with an improved property of interest, such as an increasedinsecticidal activity. Strategies for such DNA shuffling are known inthe art. See, for example, Stemmer, (1994) i Proc. Natl. Acad. Sci. USA91:10747-10751; Stemmer, (1994) Nature 370:389-391; Crameri, et al.,(1997) Nature Biotech. 15:436-438; Moore, et al., (1997) J. Mol. Biol.272:336-347; Zhang, et al., (1997) Proc. Natl. Acad. Sci. USA94:4504-4509; Crameri, et al., (1998) Nature 391:288-291; and U.S. Pat.Nos. 5,605,793 and 5,837,458.

Domain swapping or shuffling is another mechanism for generating alteredPIP-72 polypeptides. Domains may be swapped between PIP-72 polypeptides,resulting in hybrid or chimeric toxins with improved insecticidalactivity or target spectrum. Methods for generating recombinant proteinsand testing them for pesticidal activity are well known in the art (see,for example, Naimov, et al., (2001) Appl. Environ. Microbiol.67:5328-5330; de Maagd, et al., (1996) Appl. Environ. Microbiol.62:1537-1543; Ge, et al., (1991) J. Biol. Chem. 266:17954-17958;Schnepf, et al., (1990) J. Biol. Chem. 265:20923-20930; Rang, et al.,91999) Appl. Environ. Microbiol. 65:2918-2925).

Both DNA shuffling and site-directed mutagenesis were used to definepolypeptide sequences that possess pesticidal activity. DNA shufflingwas used to generate a library of active variants by recombination ofthe diversity present in GBP_A3175 (SEQ ID NO: 20) and PIP-72Da (SEQ IDNO: 10). The person skilled in the art will be able to use comparisonsto other proteins or functional assays to further define motifs. Highthroughput screening can be used to test variations of those motifs todetermine the role of specific residues. Given that knowledge forseveral motifs, one can then define the requirements for a functionalprotein. Knowledge of the motifs allows the skilled artisan to designsequence variations that would not impact function.

Alignment of homologs of PIP-72 homologs allowed identification ofresidues that are conserved among homologs in this family. Saturationmutagenesis was used to make and test substitutions at selected aminoacid positions. These mutants were tested for activity and a number ofactive substitutions not present among the homologues were identifiedproviding an understanding of the functional constraints at theseresidues.

Silencing Elements

Silencing elements are provided which, when ingested by the pest,decrease the expression of one or more of the target sequences andthereby controls the pest (i.e., has insecticidal activity).

By “silencing element” is intended a polynucleotide which when contactedby or ingested by a plant insect pest, is capable of reducing oreliminating the level or expression of a target polynucleotide or thepolypeptide encoded thereby, and a silencing element may include apolynucleotide that encodes the polynucleotide which when contacted byor ingested by a pest, is capable of reducing or eliminating the levelor expression of a target polynucleotide or the polypeptide encodedthereby. Accordingly, it is to be understood that “silencing element,”as used herein, comprises polynucleotides such as RNA constructs, DNAconstructs that encode the RNA constructs, expression constructscomprising the DNA constructs. In one embodiment, the silencing elementemployed can reduce or eliminate the expression level of the targetsequence by influencing the level of the target RNA transcript or,alternatively, by influencing translation and thereby affecting thelevel of the encoded polypeptide. Methods to assay for functionalsilencing elements that are capable of reducing or eliminating the levelof a sequence of interest are disclosed elsewhere herein. A singlepolynucleotide employed in the disclosed methods can comprise one ormore silencing elements to the same or different target polynucleotides.The silencing element can be produced in vivo (i.e., in a host cell suchas a plant or microorganism) or in vitro. It is to be understood that“silencing element,” as used herein, is intended to comprisepolynucleotides such as RNA constructs, DNA constructs that encode theRNA constructs, and/or expression constructs comprising the DNAconstructs.

As used herein, a “target sequence” or “target polynucleotide” comprisesany sequence in the pest that one desires to reduce the level ofexpression thereof. In specific embodiments, decreasing the level of thetarget sequence in the pest controls the pest. For instance, the targetsequence may be essential for growth and development. As exemplifiedelsewhere herein, decreasing the level of expression of one or more ofthese target sequences in a Coleopteran plant pest or a Diabrotica plantpest controls the pest. In some embodiments, a target polynucleotidecomprises SEQ ID NO: 981, 992, 993, 994, or 995.

In specific embodiments, a silencing element may comprise a chimericconstruction molecule comprising two or more disclosed sequences. Forexample, the chimeric construction may be a hairpin or dsRNA asdisclosed herein. A chimera may comprise two or more disclosedsequences. In one embodiment, a chimera contemplates two complementarysequences set forth herein having some degree of mismatch between thecomplementary sequences such that the two sequences are not perfectcomplements of one another. Providing at least two different sequencesin a single silencing element may allow for targeting multiple genesusing one silencing element and/or for example, one expression cassette.Targeting multiple genes may allow for slowing or reducing thepossibility of resistance by the pest. In addition, providing multipletargeting ability in one expressed molecule may reduce the expressionburden of the transformed plant or plant product, or provide topicaltreatments that are capable of targeting multiple hosts with oneapplication.

In specific embodiments, the target sequence is not endogenous to theplant. In other embodiments, while the silencing element controls pests,preferably the silencing element has no effect on the normal plant orplant part.

As discussed in further detail, silencing elements can include, but arenot limited to, a sense suppression element, an antisense suppressionelement, a double stranded RNA, a siRNA, a miRNA, or a hairpinsuppression element. The silencing element can further compriseadditional sequences that advantageously effect transcription and/or thestability of a resulting transcript. For example, the silencing elementscan comprise at least one thymine residue at the 3′ end. This can aid instabilization. Thus, the silencing elements can have at least 1, 2, 3,4, 5, 6, 7, 8, 9, 10 or more thymine residues at the 3′ end. Asdiscussed in further detail below, enhancer suppressor elements can alsobe employed in conjunction with the silencing elements disclosed herein.

In an embodiment, silencing elements may comprise a chimera where two ormore disclosed sequences or active fragments or variants, or complementsthereof, are found in the same RNA molecule. In various embodiments, adisclosed sequence or active fragment or variant, or complement thereof,may be present as more than one copy in a DNA construct, silencingelement, DNA molecule or RNA molecule. In a hairpin or dsRNA molecule,the location of a sense or antisense sequence in the molecule, forexample, in which sequence is transcribed first or is located on aparticular terminus of the RNA molecule, is not limiting to thedisclosed sequences, and the dsRNA is not to be limited by disclosuresherein of a particular location for such a sequence.

By “reduces” or “reducing” the expression level of a polynucleotide or apolypeptide encoded thereby is intended to mean, the polynucleotide orpolypeptide level of the target sequence is statistically lower than thepolynucleotide level or polypeptide level of the same target sequence inan appropriate control pest which is not exposed to (i.e., has notingested) the silencing element. In particular embodiments of theinvention, reducing the polynucleotide level and/or the polypeptidelevel of the target sequence in a pest according to the inventionresults in less than 95%, less than 90%, less than 80%, less than 70%,less than 60%, less than 50%, less than 40%, less than 30%, less than20%, less than 10%, or less than 5% of the polynucleotide level, or thelevel of the polypeptide encoded thereby, of the same target sequence inan appropriate control pest.

i. Sense Suppression Elements

As used herein, a “sense suppression element” comprises a polynucleotidedesigned to express an RNA molecule corresponding to at least a part ofa target messenger RNA in the “sense” orientation. Expression of the RNAmolecule comprising the sense suppression element reduces or eliminatesthe level of the target polynucleotide or the polypeptide encodedthereby. The polynucleotide comprising the sense suppression element maycorrespond to all or part of the sequence of the target polynucleotide,all or part of the 5′ and/or 3′ untranslated region of the targetpolynucleotide, all or part of the coding sequence of the targetpolynucleotide, or all or part of both the coding sequence and theuntranslated regions of the target polynucleotide.

Typically, a sense suppression element has substantial sequence identityto the target polynucleotide, typically greater than about 65% sequenceidentity, greater than about 85% sequence identity, about 90%, 91%, 92%,93%, 94%, 95%, 96%, 97%, 98% or 99% sequence identity. See, U.S. Pat.Nos. 5,283,184 and 5,034,323; herein incorporated by reference. Thesense suppression element can be any length so long as it allows for thesuppression of the targeted sequence. The sense suppression element canbe, for example, 15, 16, 17, 18, 19, 20, 22, 25, 30, 50, 100, 150, 200,250, 300, 350, 400, 450, 500, 600, 700, 900, 1000, 1100, 1200, 1300nucleotides or longer of the target polynucleotides. In otherembodiments, the sense suppression element can be, for example, about15-25, 19-35, 19-50, 25-100, 100-150, 150-200, 200-250, 250-300,300-350, 350-400, 450-500, 500-550, 550-600, 600-650, 650-700, 700-750,750-800, 800-850, 850-900, 900-950, 950-1000, 1000-1050, 1050-1100,1100-1200, 1200-1300, 1300-1400, 1400-1500, 1500-1600, 1600-1700,1700-1800 nucleotides or longer of the target polynucleotides.

ii. Antisense Suppression Elements

As used herein, an “antisense suppression element” comprises apolynucleotide which is designed to express an RNA moleculecomplementary to all or part of a target messenger RNA. Expression ofthe antisense RNA suppression element reduces or eliminates the level ofthe target polynucleotide. The polynucleotide for use in antisensesuppression may correspond to all or part of the complement of thesequence encoding the target polynucleotide, all or part of thecomplement of the 5′ and/or 3′ untranslated region of the targetpolynucleotide, all or part of the complement of the coding sequence ofthe target polynucleotide, or all or part of the complement of both thecoding sequence and the untranslated regions of the targetpolynucleotide. In addition, the antisense suppression element may befully complementary (i.e., 100% identical to the complement of thetarget sequence) or partially complementary (i.e., less than 100%identical to the complement of the target sequence) to the targetpolynucleotide. In specific embodiments, the antisense suppressionelement comprises at least 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%,98%, or 99% sequence complementarity to the target polynucleotide.Antisense suppression may be used to inhibit the expression of multipleproteins in the same plant. See, for example, U.S. Pat. No. 5,942,657.Furthermore, the antisense suppression element can be complementary to aportion of the target polynucleotide. Generally, sequences of at least15, 16, 17, 18, 19, 20, 22, 25, 50, 100, 200, 300, 400, 450 nucleotidesor greater of the sequence set forth in any of the targetpolynucleotides may be used. Methods for using antisense suppression toinhibit the expression of endogenous genes in plants are described, forexample, in Liu et al (2002) Plant Physiol. 129:1732-1743 and U.S. Pat.Nos. 5,759,829 and 5,942,657, each of which is herein incorporated byreference.

iii. Double Stranded RNA Suppression Element

A “double stranded RNA silencing element” or “dsRNA” comprises at leastone transcript that is capable of forming a dsRNA either before or afteringestion by a pest. Thus, a “dsRNA silencing element” includes a dsRNA,a transcript or polyribonucleotide capable of forming a dsRNA or morethan one transcript or polyribonucleotide capable of forming a dsRNA.“Double stranded RNA” or “dsRNA” refers to a polyribonucleotidestructure formed either by a single self-complementary RNA molecule or apolyribonucleotide structure formed by the expression of least twodistinct RNA strands. The dsRNA molecule(s) employed in the methods andcompositions of the invention mediate the reduction of expression of atarget sequence, for example, by mediating RNA interference “RNAi” orgene silencing in a sequence-specific manner. In the context of thepresent invention, the dsRNA is capable of reducing or eliminating thelevel or expression of at least one target polynucleotide or polypeptideencoded thereby in a pest.

The dsRNA can reduce or eliminate the expression level of the targetsequence by influencing the level of the target RNA transcript, byinfluencing translation and thereby affecting the level of the encodedpolypeptide, or by influencing expression at the pre-transcriptionallevel (i.e., via the modulation of chromatin structure, methylationpattern, etc., to alter gene expression). See, for example, Verdel etal. (2004) Science 303:672-676; Pal-Bhadra et al. (2004) Science303:669-672; Allshire (2002) Science 297:1818-1819; Volpe et al. (2002)Science 297:1833-1837; Jenuwein (2002) Science 297:2215-2218; and Hallet al. (2002) Science 297:2232-2237. Methods to assay for functionaldsRNA that are capable of reducing or eliminating the level of asequence of interest are disclosed elsewhere herein. Accordingly, asused herein, the term “dsRNA” is meant to encompass other terms used todescribe nucleic acid molecules that are capable of mediating RNAinterference or gene silencing, including, for example,short-interfering RNA (siRNA), double-stranded RNA (dsRNA), micro-RNA(miRNA), hairpin RNA, short hairpin RNA (shRNA), post-transcriptionalgene silencing RNA (ptgsRNA), and others.

In specific embodiments, at least one strand of the duplex ordouble-stranded region of the dsRNA shares sufficient sequence identityor sequence complementarity to the target polynucleotide to allow forthe dsRNA to reduce the level of expression of the target sequence. Asused herein, the strand that is complementary to the targetpolynucleotide is the “antisense strand” and the strand homologous tothe target polynucleotide is the “sense strand.”

In another embodiment, the dsRNA comprises a hairpin RNA. A hairpin RNAcomprises an RNA molecule that is capable of folding back onto itself toform a double stranded structure. Multiple structures can be employed ashairpin elements. In specific embodiments, the dsRNA suppression elementcomprises a hairpin element which comprises in the following order, afirst segment, a second segment, and a third segment, where the firstand the third segment share sufficient complementarity to allow thetranscribed RNA to form a double-stranded stem-loop structure.

The “second segment” of the hairpin comprises a “loop” or a “loopregion.” These terms are used synonymously herein and are to beconstrued broadly to comprise any nucleotide sequence that confersenough flexibility to allow self-pairing to occur between complementaryregions of a polynucleotide (i.e., segments 1 and 3 which form the stemof the hairpin). For example, in some embodiments, the loop region maybe substantially single stranded and act as a spacer between theself-complementary regions of the hairpin stem-loop. In someembodiments, the loop region can comprise a random or nonsensenucleotide sequence and thus not share sequence identity to a targetpolynucleotide. In other embodiments, the loop region comprises a senseor an antisense RNA sequence or fragment thereof that shares identity toa target polynucleotide. See, for example, International PatentPublication No. WO 02/00904, herein incorporated by reference. Inspecific embodiments, the loop region can be optimized to be as short aspossible while still providing enough intramolecular flexibility toallow the formation of the base-paired stem region. Accordingly, theloop sequence is generally less than 1000, 900, 800, 700, 600, 500, 400,300, 200, 100, 50, 25, 20, 19, 18, 17, 16, 15, 10 nucleotides or less.

The “first” and the “third” segment of the hairpin RNA molecule comprisethe base-paired stem of the hairpin structure. The first and the thirdsegments are inverted repeats of one another and share sufficientcomplementarity to allow the formation of the base-paired stem region.In specific embodiments, the first and the third segments are fullycomplementary to one another. Alternatively, the first and the thirdsegment may be partially complementary to each other so long as they arecapable of hybridizing to one another to form a base-paired stem region.The amount of complementarity between the first and the third segmentcan be calculated as a percentage of the entire segment. Thus, the firstand the third segment of the hairpin RNA generally share at least 50%,60%, 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, upto and including 100% complementarity.

The first and the third segment are at least about 1000, 500, 475, 450,425, 400, 375, 350, 325, 300, 250, 225, 200, 175, 150, 125, 100, 75, 60,50, 40, 30, 25, 22, 20, 19, 18, 17, 16, 15 or 10 nucleotides in length.In specific embodiments, the length of the first and/or the thirdsegment is about 10-100 nucleotides, about 10 to about 75 nucleotides,about 10 to about 50 nucleotides, about 10 to about 40 nucleotides,about 10 to about 35 nucleotides, about 10 to about 30 nucleotides,about 10 to about 25 nucleotides, about 10 to about 19 nucleotides,about 10 to about 20 nucleotides, about 19 to about 50 nucleotides,about 50 nucleotides to about 100 nucleotides, about 100 nucleotides toabout 150 nucleotides, about 100 nucleotides to about 300 nucleotides,about 150 nucleotides to about 200 nucleotides, about 200 nucleotides toabout 250 nucleotides, about 250 nucleotides to about 300 nucleotides,about 300 nucleotides to about 350 nucleotides, about 350 nucleotides toabout 400 nucleotides, about 400 nucleotide to about 500 nucleotides,about 600 nt, about 700 nt, about 800 nt, about 900 nt, about 1000 nt,about 1100 nt, about 1200 nt, 1300 nt, 1400 nt, 1500 nt, 1600 nt, 1700nt, 1800 nt, 1900 nt, 2000 nt or longer. In other embodiments, thelength of the first and/or the third segment comprises at least 10-19nucleotides, 10-20 nucleotides; 19-35 nucleotides, 20-35 nucleotides;30-45 nucleotides; 40-50 nucleotides; 50-100 nucleotides; 100-300nucleotides; about 500 -700 nucleotides; about 700-900nucleotides; about900-1100 nucleotides; about 1300 -1500 nucleotides; about 1500 -1700nucleotides; about 1700 -1900 nucleotides; about 1900 -2100 nucleotides;about 2100 -2300 nucleotides; or about 2300 -2500 nucleotides. See, forexample, International Application Publication No. W002/00904. Inspecific embodiments, the first and the third segment comprise at least20 nucleotides having at least 85% complementary to the first segment.In still other embodiments, the first and the third segments which formthe stem-loop structure of the hairpin comprises 3′ or 5′ overhangregions having unpaired nucleotide residues.

The disclosed hairpin molecules or double-stranded RNA molecules mayhave more than one target sequence or active fragments or variants, orcomplements thereof, found in the same portion of the RNA molecule. Forexample, in a chimeric hairpin structure, the first segment of a hairpinmolecule comprises two polynucleotide sections, each with a differenttarget sequence. For example, reading from one terminus of the hairpin,the first segment is composed of sequences from two separate genes (Afollowed by B). This first segment is followed by the second segment,the loop portion of the hairpin. The loop segment is followed by thethird segment, where the complementary strands of the sequences in thefirst segment are found (B* followed by A*) in forming the stem-loop,hairpin structure, the stem contains SeqA-A* at the distal end of thestem and SeqB-B* proximal to the loop region.

In specific embodiments, the sequences used in the first, the second,and/or the third segments comprise domains that are designed to havesufficient sequence identity to a target polynucleotide of interest andthereby have the ability to decrease the level of expression of thetarget polynucleotide. The specificity of the inhibitory RNA transcriptsis therefore generally conferred by these domains of the silencingelement. Thus, in some embodiments, the first, second and/or thirdsegment of the silencing element comprise a domain having at least 10,at least 15, at least 19, at least 20, at least 21, at least 22, atleast 23, at least 24, at least 25, at least 30, at least 40, at least50, at least 100, at least 200, at least 300, at least 500, at least1000, or more than 1000 nucleotides that share sufficient sequenceidentity to the target polynucleotide to allow for a decrease inexpression levels of the target polynucleotide when expressed in anappropriate cell. In other embodiments, the domain is between about 15to 50 nucleotides, about 19-35 nucleotides, about 20-35 nucleotides,about 25-50 nucleotides, about 19 to 75 nucleotides, about 20 to 75nucleotides, about 40-90 nucleotides about 15-100 nucleotides, 10-100nucleotides, about 10 to about 75 nucleotides, about 10 to about 50nucleotides, about 10 to about 40 nucleotides, about 10 to about 35nucleotides, about 10 to about 30 nucleotides, about 10 to about 25nucleotides, about 10 to about 20 nucleotides, about 10 to about 19nucleotides, about 50 nucleotides to about 100 nucleotides, about 100nucleotides to about 150 nucleotides, about 150 nucleotides to about 200nucleotides, about 200 nucleotides to about 250 nucleotides, about 250nucleotides to about 300 nucleotides, about 300 nucleotides to about 350nucleotides, about 350 nucleotides to about 400 nucleotides, about 400nucleotide to about 500 nucleotides or longer. In other embodiments, thelength of the first and/or the third segment comprises at least 10-20nucleotides, at least 10-19 nucleotides, 20-35 nucleotides, 30-45nucleotides, 40-50 nucleotides, 50-100 nucleotides, or about 100-300nucleotides.

In specific embodiments, the domain of the first, the second, and/or thethird segment has 100% sequence identity to the target polynucleotide.In other embodiments, the domain of the first, the second and/or thethird segment having homology to the target polypeptide have at least50%, 60%, 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%,99%, or greater sequence identity to a region of the targetpolynucleotide. The sequence identity of the domains of the first, thesecond and/or the third segments to the target polynucleotide need onlybe sufficient to decrease expression of the target polynucleotide ofinterest. See, for example, Chuang and Meyerowitz (2000) Proc. Natl.Acad. Sci. USA 97:4985-4990; Stoutjesdijk et al. (2002) Plant Physiol.129:1723-1731; Waterhouse and Helliwell (2003) Nat. Rev. Genet. 4:29-38;Pandolfini et al. BMC Biotechnology 3:7, and U.S. Patent Publication No.20030175965; each of which is herein incorporated by reference. Atransient assay for the efficiency of hpRNA constructs to silence geneexpression in vivo has been described by Panstruga et al. (2003) Mol.Biol. Rep. 30:135-140.

The amount of complementarity shared between the first, second, and/orthird segment and the target polynucleotide or the amount ofcomplementarity shared between the first segment and the third segment(i.e., the stem of the hairpin structure) may vary depending on theorganism in which gene expression is to be controlled. Some organisms orcell types may require exact pairing or 100% identity, while otherorganisms or cell types may tolerate some mismatching. In some cells,for example, a single nucleotide mismatch in the targeting sequenceabrogates the ability to suppress gene expression. In these cells, thedisclosed suppression cassettes can be used to target the suppression ofmutant genes, for example, oncogenes whose transcripts comprise pointmutations and therefore they can be specifically targeted using themethods and compositions disclosed herein without altering theexpression of the remaining wild-type allele. In other organisms,holistic sequence variability may be tolerated as long as some 22 ntregion of the sequence is represented in 100% homology between targetpolynucleotide and the suppression cassette.

In other embodiments, the silencing element can comprise a small RNA(sRNA). sRNAs can comprise both micro RNA (miRNA) and short-interferingRNA (siRNA) (Meister and Tuschl (2004) Nature 431:343-349 and Bonetta etal. (2004) Nature Methods 1:79-86). miRNAs are regulatory agentscomprising about 19 to about 24 ribonucleotides in length which arehighly efficient at inhibiting the expression of target polynucleotides.See, for example Javier et al. 10 (2003) Nature 425: 257-263, hereinincorporated by reference. For miRNA interference, the silencing elementcan be designed to express a dsRNA molecule that forms a hairpinstructure or partially base-paired structure containing 19, 20, 21, 22,23, 24 or 25 -nucleotide sequence that is complementary to the targetpolynucleotide of interest. The miRNA can be synthetically made, ortranscribed as a longer RNA which is subsequently cleaved to produce theactive miRNA. 15 Specifically, the miRNA can comprise 19 nucleotides ofthe sequence having homology to a target polynucleotide in senseorientation and 19 nucleotides of a corresponding antisense sequencethat is complementary to the sense sequence. The miRNA can be an“artificial miRNA” or “amiRNA” which comprises a miRNA sequence that issynthetically designed to silence a target sequence.

The methods and compositions disclosed herein employ silencing elementsthat when transcribed “form” a dsRNA molecule. Accordingly, theheterologous polynucleotide being expressed need not form the dsRNA byitself, but can interact with other sequences in the plant cell or inthe pest gut after ingestion to allow the formation of the dsRNA. Forexample, a chimeric polynucleotide that can selectively silence thetarget polynucleotide can be generated by expressing a chimericconstruct comprising the target sequence for a miRNA or siRNA to asequence corresponding to all or part of the gene or genes to besilenced. In this embodiment, the dsRNA is “formed” when the target forthe miRNA or siRNA interacts with the miRNA present in the cell. Theresulting dsRNA can then reduce the level of expression of the gene orgenes to be silenced. See, for example, US Patent ApplicationPublication Number 2007-0130653, entitled “Methods and Compositions forGene Silencing.” The construct can be designed to have a target for anendogenous miRNA or alternatively, a target for a heterologous and/orsynthetic miRNA can be employed in the construct. If a heterologousand/or synthetic miRNA is employed, it can be introduced into the cellon the same nucleotide construct as the chimeric polynucleotide or on aseparate construct. As discussed elsewhere herein, any method can beused to introduce the construct comprising the heterologous miRNA.

As used herein, by “controlling a pest” or “controls a pest” is intendedany affect on a pest that results in limiting the damage that the pestcauses. Controlling a pest includes, but is not limited to, killing thepest, inhibiting development of the pest, altering fertility or growthof the pest in such a manner that the pest provides less damage to theplant, decreasing the number of offspring produced, producing less fitpests, producing pests more susceptible to predator attack, or deterringthe pests from eating the plant.

Reducing the level of expression of the target polynucleotide or thepolypeptide encoded thereby, in the pest results in the suppression,control, and/or killing the invading pathogenic organism. Reducing thelevel of expression of the target sequence of the pest will reduce thedisease symptoms resulting from pathogen challenge by at least about 2%to at least about 6%, at least about 5% to about 50%, at least about 10%to about 60%, at least about 30% to about 70%, at least about 40% toabout 80%, or at least about 50% to about 90% or greater. Hence, themethods of the invention can be utilized to control pests, particularly,Coleopteran plant pest or a Diabrotica plant pest.

Assays that measure the control of a pest are commonly known in the art,as are methods to quantitate disease resistance in plants followingpathogen infection. See, for example, U.S. Pat. No. 5,614,395, hereinincorporated by reference. Such techniques include, measuring over time,the average lesion diameter, the pathogen biomass, and the overallpercentage of decayed plant tissues. See, for example, Thomma et al.(1998) Plant Biology 95:15107-15111, herein incorporated by reference.See, also Baum et al. (2007) Nature Biotech 11:1322-1326 and WO2007/035650 which proved both whole plant feeding assays and corn rootfeeding assays. Both of these references are herein incorporated byreference in their entirety.

Compositions

Compositions comprising a PIP-72 polypeptide and a silencing element arealso embraced. In some embodiments the composition comprises a RyanR(SEQ ID NO: 992), HP2 SEQ ID NO: 994), or RPS10 (SEQ ID NO: 995) targetsilencing element. In one embodiment, the composition comprises a PIP-72polypeptide and a silencing element, wherein the silencing elementcomprises any one of SEQ ID NOs: 982-991, 993, or SEQ ID NOs: 561-572 ofUS Patent Application Publication No. US2014/0275208 and US2015/0257389.

One or more of the polynucleotides comprising the silencing element canbe provided as an external composition such as a spray or powder to theplant, plant part, seed, a plant insect pest, or an area of cultivation.It is recognized that the composition can comprise a cell (such as plantcell or a bacterial cell), in which a polynucleotide encoding a PIP-72and a silencing element is stably incorporated into the genome andoperably linked to promoters active in the cell. In other embodiments,compositions comprising the PIP-72 and a silencing element are notcontained in a cell. In such embodiments, the composition can be appliedto an area inhabited by a plant insect pest. In one embodiment, thecomposition is applied externally to a plant (i.e., by spraying a fieldor area of cultivation) to protect the plant from the pest. Methods ofapplying nucleotides in such a manner are known to those of skill in theart.

The composition of the invention can further be formulated as bait. Inthis embodiment, the compositions comprise a food substance or anattractant which enhances the attractiveness of the composition to thepest.

The composition comprising a PIP-72 and a silencing element can beformulated in an agriculturally suitable and/or environmentallyacceptable carrier. Such carriers can be any material that the animal,plant or environment to be treated can tolerate. Furthermore, thecarrier must be such that the composition remains effective atcontrolling a plant insect pest. Examples of such carriers includewater, saline, Ringer's solution, dextrose or other sugar solutions,Hank's solution, and other aqueous physiologically balanced saltsolutions, phosphate buffer, bicarbonate buffer and Tris buffer. Inaddition, the composition may include compounds that increase thehalf-life of a composition. Various insecticidal formulations can alsobe found in, for example, US Patent Application Publication Numbers2008/0275115, 2008/0242174, 2008/0027143, 2005/0042245, and2004/0127520, each of which is herein incorporated by reference.

Nucleotide Constructs, Expression Cassettes and Vectors

The use of the term “nucleotide constructs” herein is not intended tolimit the embodiments to nucleotide constructs comprising DNA. Those ofordinary skill in the art will recognize that nucleotide constructsparticularly polynucleotides and oligonucleotides composed ofribonucleotides and combinations of ribonucleotides anddeoxyribonucleotides may also be employed in the methods disclosedherein. The nucleotide constructs, nucleic acids, and nucleotidesequences of the embodiments additionally encompass all complementaryforms of such constructs, molecules, and sequences. Further, thenucleotide constructs, nucleotide molecules, and nucleotide sequences ofthe embodiments encompass all nucleotide constructs, molecules, andsequences which can be employed in the methods of the embodiments fortransforming plants including, but not limited to, those comprised ofdeoxyribonucleotides, ribonucleotides, and combinations thereof. Suchdeoxyribonucleotides and ribonucleotides include both naturallyoccurring molecules and synthetic analogues. The nucleotide constructs,nucleic acids, and nucleotide sequences of the embodiments alsoencompass all forms of nucleotide constructs including, but not limitedto, single-stranded forms, double-stranded forms, hairpins,stem-and-loop structures and the like.

A further embodiment relates to a transformed organism such as anorganism selected from plant and insect cells, bacteria, yeast,baculovirus, protozoa, nematodes and algae. The transformed organismcomprises a DNA molecule of the embodiments, an expression cassettecomprising the DNA molecule or a vector comprising the expressioncassette, which may be stably incorporated into the genome of thetransformed organism.

The sequences of the embodiments are provided in DNA constructs forexpression in the organism of interest. The construct will include 5′and 3′ regulatory sequences operably linked to a sequence of theembodiments. The term “operably linked” as used herein refers to afunctional linkage between a promoter and a second sequence, wherein thepromoter sequence initiates and mediates transcription of the DNAsequence corresponding to the second sequence. Generally, operablylinked means that the nucleic acid sequences being linked are contiguousand where necessary to join two protein coding regions in the samereading frame. The construct may additionally contain at least oneadditional gene to be cotransformed into the organism. Alternatively,the additional gene(s) can be provided on multiple DNA constructs.

The DNA construct will generally include in the 5′ to 3′ direction oftranscription: a transcriptional and translational initiation region(i.e., a promoter), a DNA sequence of the embodiments, and atranscriptional and translational termination region (i.e., terminationregion) functional in the organism serving as a host. Thetranscriptional initiation region (i.e., the promoter) may be native,analogous, foreign or heterologous to the host organism and/or to thesequence of the embodiments. Additionally, the promoter may be thenatural sequence or alternatively a synthetic sequence. The term“foreign” as used herein indicates that the promoter is not found in thenative organism into which the promoter is introduced. Where thepromoter is “foreign” or “heterologous” to the sequence of theembodiments, it is intended that the promoter is not the native ornaturally occurring promoter for the operably linked sequence of theembodiments. Where the promoter is a native or natural sequence, theexpression of the operably linked sequence is altered from the wild-typeexpression, which results in an alteration in phenotype.

The polynucleotide encoding the silencing element or in specificembodiments employed in the disclosed methods and compositions can beprovided in expression cassettes for expression in a plant or organismof interest. It is recognized that multiple silencing elements includingmultiple identical silencing elements, multiple silencing elementstargeting different regions of the target sequence, or multiplesilencing elements from different target sequences can be used. In thisembodiment, it is recognized that each silencing element can becontained in a single or separate cassette, DNA construct, or vector. Asdiscussed, any means of providing the silencing element is contemplated.

In other embodiment, the double stranded RNA is expressed from asuppression cassette. Such a cassette can comprise two convergentpromoters that drive transcription of an operably linked silencingelement. “Convergent promoters” refers to promoters that are oriented oneither terminus of the operably linked silencing element such that eachpromoter drives transcription of the silencing element in oppositedirections, yielding two transcripts. In such embodiments, theconvergent promoters allow for the transcription of the sense andanti-sense strand and thus allow for the formation of a dsRNA. Such acassette may also comprise two divergent promoters that drivetranscription of one or more operably linked silencing elements.“Divergent promoters” refers to promoters that are oriented in oppositedirections of each other, driving transcription of the one or moresilencing elements in opposite directions. In such embodiments, thedivergent promoters allow for the transcription of the sense andantisense strands and allow for the formation of a dsRNA. In suchembodiments, the divergent promoters also allow for the transcription ofat least two separate hairpin RNAs. In another embodiment, one cassettecomprising two or more silencing elements under the control of twoseparate promoters in the same orientation is present in a construct. Inanother embodiment, two or more individual cassettes, each comprising atleast one silencing element under the control of a promoter, are presentin a construct in the same orientation.

In some embodiments the DNA construct may also include a transcriptionalenhancer sequence. As used herein, the term an “enhancer” refers to aDNA sequence which can stimulate promoter activity, and may be an innateelement of the promoter or a heterologous element inserted to enhancethe level or tissue-specificity of a promoter. Various enhancers areknown in the art including for example, introns with gene expressionenhancing properties in plants (US Patent Application Publication Number2009/0144863, the ubiquitin intron (i.e., the maize ubiquitin intron 1(see, for example, NCBI sequence S94464; Christensen and Quail (1996)Transgenic Res. 5:213-218; Christensen et al. (1992) Plant MolecularBiology 18:675-689)), the omega enhancer or the omega prime enhancer(Gallie, et al., (1989) Molecular Biology of RNA ed. Cech (Liss, NewYork) 237-256 and Gallie, et al., (1987) Gene 60:217-25), the CaMV 35Senhancer (see, e.g., Benfey, et al., (1990) EMBO J. 9:1685-96), themaize Adhl intron (Kyozuka et al. (1991) Mol. Gen. Genet. 228:40-48;Kyozuka et al. (1990) Maydica 35:353-357), the enhancers of U.S. Pat.No. 7,803,992, and the sugarcane bacilliform viral (SCBV) enhancer ofWO2013130813 may also be used, each of which is incorporated byreference. The above list of transcriptional enhancers is not meant tobe limiting. Any appropriate transcriptional enhancer can be used in theembodiments.

In some embdodiments, a DNA construct comprises polynucleotides encodingPIP-72 polypeptide and a silencing element. In one embodiment, a DNAconstruct comprises polynucleotides encoding a PIP-72 polypeptide and asilencing element, wherein the silencing element targets RyanR (SEQ IDNO: 992), HP2 SEQ ID NO: 994), or RPS10 (SEQ ID NO: 995). In anotherembodiment, a DNA construct comprises polynucleotides encoding a PIP-72polypeptide and a silencing element, wherein the silencing elementcomprises any one of SEQ ID NOs: 982-991, 993, or SEQ ID NOs: 561-572 ofUS Patent Application Publication No. US2014/0275208 and US2015/0257389.

The termination region may be native with the transcriptional initiationregion, may be native with the operably linked DNA sequence of interest,may be native with the plant host or may be derived from another source(i.e., foreign or heterologous to the promoter, the sequence ofinterest, the plant host or any combination thereof).

Convenient termination regions are available from the Ti-plasmid of A.tumefaciens, such as the octopine synthase and nopaline synthasetermination regions. See also, Guerineau, et al., (1991) Mol. Gen.Genet. 262:141-144; Proudfoot, (1991) Cell 64:671-674; Sanfacon, et al.,(1991) Genes Dev. 5:141-149; Mogen, et al., (1990) Plant Cell2:1261-1272; Munroe, et al., (1990) Gene 91:151-158; Ballas, et al.,(1989) Nucleic Acids Res. 17:7891-7903 and Joshi, et al., (1987) NucleicAcid Res. 15:9627-9639.

Where appropriate, a nucleic acid may be optimized for increasedexpression in the host organism. Thus, where the host organism is aplant, the synthetic nucleic acids can be synthesized usingplant-preferred codons for improved expression. See, for example,Campbell and Gowri, (1990) Plant Physiol. 92:1-11 for a discussion ofhost-preferred codon usage. For example, although nucleic acid sequencesof the embodiments may be expressed in both monocotyledonous anddicotyledonous plant species, sequences can be modified to account forthe specific codon preferences and GC content preferences ofmonocotyledons or dicotyledons as these preferences have been shown todiffer (Murray et al. (1989) Nucleic Acids Res. 17:477-498). Thus, themaize-preferred codon for a particular amino acid may be derived fromknown gene sequences from maize. Maize codon usage for 28 genes frommaize plants is listed in Table 4 of Murray, et al., supra. Methods areavailable in the art for synthesizing plant-preferred genes. See, forexample, U.S. Pat. Nos. 5,380,831, and 5,436,391 and Murray, et al.,(1989) Nucleic Acids Res. 17:477-498, and Liu H et al. Mol Bio Rep37:677-684, 2010, herein incorporated by reference. A Zea maize codonusage table can be found atkazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=4577, which can beaccessed using the www prefix.

A Glycine max codon usage table can be found atkazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=3847&aa=1&style=N,which can be accessed using the www prefix.

In some embodiments the recombinant nucleic acid molecule encoding aPIP-72 polypeptide has maize optimized codons.

Additional sequence modifications are known to enhance gene expressionin a cellular host. These include elimination of sequences encodingspurious polyadenylation signals, exon-intron splice site signals,transposon-like repeats, and other well-characterized sequences that maybe deleterious to gene expression. The GC content of the sequence may beadjusted to levels average for a given cellular host, as calculated byreference to known genes expressed in the host cell. The term “hostcell” as used herein refers to a cell which contains a vector andsupports the replication and/or expression of the expression vector isintended. Host cells may be prokaryotic cells such as E. coli oreukaryotic cells such as yeast, insect, amphibian or mammalian cells ormonocotyledonous or dicotyledonous plant cells. An example of amonocotyledonous host cell is a maize host cell. When possible, thesequence is modified to avoid predicted hairpin secondary mRNAstructures.

The expression cassettes may additionally contain 5′ leader sequences.Such leader sequences can act to enhance translation. Translationleaders are known in the art and include: picornavirus leaders, forexample, EMCV leader (Encephalomyocarditis 5′ noncoding region)(Elroy-Stein, et al., (1989) Proc. Natl. Acad. Sci. USA 86:6126-6130);potyvirus leaders, for example, TEV leader (Tobacco Etch Virus) (Gallie,et al., (1995) Gene 165(2):233-238), MDMV leader (Maize Dwarf MosaicVirus), human immunoglobulin heavy-chain binding protein (BiP) (Macejak,et al., (1991) Nature 353:90-94); untranslated leader from the coatprotein mRNA of alfalfa mosaic virus (AMV RNA 4) (Jobling, et al.,(1987) Nature 325:622-625); tobacco mosaic virus leader (TMV) (Gallie,et al., (1989) in Molecular Biology of RNA, ed. Cech (Liss, New York),pp. 237-256) and maize chlorotic mottle virus leader (MCMV) (Lommel, etal., (1991) Virology 81:382-385). See also, Della-Cioppa, et al., (1987)Plant Physiol. 84:965-968. Such constructs may also contain a “signalsequence” or “leader sequence” to facilitate co-translational orpost-translational transport of the peptide to certain intracellularstructures such as the chloroplast (or other plastid), endoplasmicreticulum or Golgi apparatus.

“Signal sequence” as used herein refers to a sequence that is known orsuspected to result in cotranslational or post-translational peptidetransport across the cell membrane. In eukaryotes, this typicallyinvolves secretion into the Golgi apparatus, with some resultingglycosylation. Insecticidal toxins of bacteria are often synthesized asprotoxins, which are proteolytically activated in the gut of the targetpest (Chang, (1987) Methods Enzymol. 153:507-516). In some embodiments,the signal sequence is located in the native sequence or may be derivedfrom a sequence of the embodiments. “Leader sequence” as used hereinrefers to any sequence that when translated, results in an amino acidsequence sufficient to trigger co-translational transport of the peptidechain to a subcellular organelle. Thus, this includes leader sequencestargeting transport and/or glycosylation by passage into the endoplasmicreticulum, passage to vacuoles, plastids including chloroplasts,mitochondria, and the like. Nuclear-encoded proteins targeted to thechloroplast thylakoid lumen compartment have a characteristic bipartitetransit peptide, composed of a stromal targeting signal peptide and alumen targeting signal peptide. The stromal targeting information is inthe amino-proximal portion of the transit peptide. The lumen targetingsignal peptide is in the carboxyl-proximal portion of the transitpeptide, and contains all the information for targeting to the lumen.Recent research in proteomics of the higher plant chloroplast hasachieved in the identification of numerous nuclear-encoded lumenproteins (Kieselbach et al. FEBS LETT 480:271-276, 2000; Peltier et al.Plant Cell 12:319-341, 2000; Bricker et al. Biochim. Biophys Acta1503:350-356, 2001), the lumen targeting signal peptide of which canpotentially be used in accordance with the present disclosure. About 80proteins from Arabidopsis, as well as homologous proteins from spinachand garden pea, are reported by Kieselbach et al., PhotosynthesisResearch, 78:249-264, 2003. In particular, Table 2 of this publication,which is incorporated into the description herewith by reference,discloses 85 proteins from the chloroplast lumen, identified by theiraccession number (see also US Patent Application Publication2009/09044298). In addition, the recently published draft version of therice genome (Goff et al, Science 296:92-100, 2002) is a suitable sourcefor lumen targeting signal peptide which may be used in accordance withthe present disclosure.

Suitable chloroplast transit peptides (CTP) are well known to oneskilled in the art also include chimeric CTPs comprising but not limitedto, an N-terminal domain, a central domain or a C-terminal domain from aCTP from Oryza sativa 1-deoxy-D xyulose-5-Phosphate Synthase Oryzasativa-Superoxide dismutase Oryza sativa-soluble starch synthase Oryzasativa-NADP-dependent Malic acid enzyme Oryzasativa-Phospho-2-dehydro-3-deoxyheptonate Aldolase 2 Oryzasativa-L-Ascorbate peroxidase 5 Oryza sativa-Phosphoglucan waterdikinase, Zea Mays ssRUBISCO, Zea Mays-beta-glucosidase, Zea Mays-Malatedehydrogenase, Zea Mays Thioredoxin M-type (US Patent ApplicationPublication 2012/0304336). Chloroplast transit peptides of US PatentPublications US20130205440A1, US20130205441A1 and US20130210114A1.

The PIP-72 polypeptide gene to be targeted to the chloroplast may beoptimized for expression in the chloroplast to account for differencesin codon usage between the plant nucleus and this organelle. In thismanner, the nucleic acids of interest may be synthesized usingchloroplast-preferred codons. See, for example, U.S. Pat. No. 5,380,831,herein incorporated by reference.

In preparing the expression cassette, the various DNA fragments may bemanipulated so as to provide for the DNA sequences in the properorientation and, as appropriate, in the proper reading frame. Towardthis end, adapters or linkers may be employed to join the DNA fragmentsor other manipulations may be involved to provide for convenientrestriction sites, removal of superfluous DNA, removal of restrictionsites or the like. For this purpose, in vitro mutagenesis, primerrepair, restriction, annealing, resubstitutions, e.g., transitions andtransversions, may be involved.

A number of promoters can be used in the practice of the embodiments.The promoters can be selected based on the desired outcome. The nucleicacids can be combined with constitutive, tissue-preferred, inducible orother promoters for expression in the host organism. Promoters of thepresent invention include homologues of cis elements known to effectgene regulation that show homology with the promoter sequences of thepresent invention. These cis elements include, but are not limited to,oxygen responsive cis elements (Cowen et al., J Biol. Chem.268(36):26904-26910 (1993)), light regulatory elements (Bruce andQuaill, Plant Cell 2 (11):1081-1089 (1990); Bruce et al., EMBO J.10:3015-3024 (1991); Rocholl et al., Plant Sci. 97:189-198 (1994); Blocket al., Proc. Natl. Acad. Sci. USA 87:5387-5391 (1990); Giuliano et al.,Proc. Natl. Acad. Sci. USA 85:7089-7093 (1988); Staiger et al., Proc.Natl. Acad. Sci. USA 86:6930-6934 (1989); Izawa et al., Plant Cell6:1277-1287 (1994); Menkens et al., Trends in Biochemistry 20:506-510(1995); Foster et al., FASEB J. 8:192-200 (1994); Plesse et al., Mol GenGene 254:258-266 (1997); Green et al., EMBO J. 6:2543-2549 (1987);Kuhlemeier et al., Ann. Rev Plant Physiol. 38:221-257 (1987); Villain etal., J. Biol. Chem. 271:32593-32598 (1996); Lam et al., Plant Cell2:857-866 (1990); Gilmartin et al., Plant Cell 2:369-378 (1990); Dattaet al., Plant Cell 1:1069-1077 (1989); Gilmartin et al., Plant Cell2:369-378 (1990); Castresana et al., EMBO J. 7:1929-1936 (1988); Ueda etal., Plant Cell 1:217-227 (1989); Terzaghi et al., Annu. Rev. PlantPhysiol. Plant Mol. Biol. 46:445-474 (1995); Green et al., EMBO J.6:2543-2549 (1987); Villain et al., J. Biol. Chem. 271:32593-32598(1996); Tjaden et al., Plant Cell 6:107-118 (1994); Tjaden et al., PlantPhysiol. 108:1109-1117 (1995); Ngai et al., Plant J. 12:1021-1234(1997); Bruce et al., EMBO J. 10:3015-3024 (1991); Ngai et al., Plant J.12:1021-1034 (1997)), elements responsive to gibberellin, (Muller etal., J. Plant Physiol. 145:606-613 (1995); Croissant et al., PlantScience 116:27-35 (1996); Lohmer et al., EMBO J. 10:617-624 (1991);Rogers et al., Plant Cell 4:1443-1451 (1992); Lanahan et al., Plant Cell4:203-211 (1992); Skriver et al., Proc. Natl. Acad. Sci. USA88:7266-7270 (1991); Gilmartin et al., Plant Cell 2:369-378 (1990);Huang et al., Plant Mol. Biol. 14:655-668 (1990), Gubler et al., PlantCell 7:1879-1891 (1995)), elements responsive to abscisic acid, (Busk etal., Plant Cell 9:2261-2270 (1997); Guiltinan et al., Science250:267-270 (1990); Shen et al., Plant Cell 7:295-307 (1995); Shen etal., Plant Cell 8:1107-1119 (1996); Seo et al., Plant Mol. Biol.27:1119-1131 (1995); Marcotte et al., Plant Cell 1:969-976 (1989); Shenet al., Plant Cell 7:295-307 (1995); Iwasaki et al., Mol Gen Genet247:391-398 (1995); Hattori et al., Genes Dev. 6:609-618 (1992); Thomaset al., Plant Cell 5:1401-1410 (1993)), elements similar to abscisicacid responsive elements, (Ellerstrom et al., Plant Mol. Biol.32:1019-1027 (1996)), auxin responsive elements (Liu et al., Plant Cell6:645-657 (1994); Liu et al., Plant Physiol. 115:397-407 (1997); Kosugiet al., Plant J. 7:877-886 (1995); Kosugi et al., Plant Cell 9:1607-1619(1997); Ballas et al., J. Mol. Biol. 233:580-596 (1993)), a cis elementresponsive to methyl jasmonate treatment (Beaudoin and Rothstein, PlantMol. Biol. 33:835-846 (1997)), a cis element responsive to abscisic acidand stress response (Straub et al., Plant Mol. Biol. 26:617-630 (1994)),ethylene responsive cis elements (Itzhaki et al., Proc. Natl. Acad. Sci.USA 91:8925-8929 (1994); Montgomery et al., Proc. Natl. Acad. Sci. USA90:5939-5943 (1993); Sessa et al., Plant Mol. Biol. 28:145-153 (1995);Shinshi et al., Plant Mol. Biol. 27:923-932 (1995)), salicylic acid cisresponsive elements, (Strange et al., Plant J. 11:1315-1324 (1997); Qinet al., Plant Cell 6:863-874 (1994)), a cis element that responds towater stress and abscisic acid (Lam et al., J. Biol. Chem.266:17131-17135 (1991); Thomas et al., Plant Cell 5:1401-1410 (1993);Pla et al., Plant Mol Biol 21:259-266 (1993)), a cis element essentialfor M phase-specific expression (Ito et al., Plant Cell 10:331-341(1998)), sucrose responsive elements (Huang et al., Plant Mol. Biol.14:655-668 (1990); Hwang et al., Plant Mol Biol 36:331-341 (1998);Grierson et al., Plant J. 5:815-826 (1994)), heat shock responseelements (Pelham et al., Trends Genet. 1:31-35 (1985)), elementsresponsive to auxin and/or salicylic acid and also reported for lightregulation (Lam et al., Proc. Natl. Acad. Sci. USA 86:7890-7897 (1989);Benfey et al., Science 250:959-966 (1990)), elements responsive toethylene and salicylic acid (Ohme-Takagi et al., Plant Mol. Biol.15:941-946 (1990)), elements responsive to wounding and abiotic stress(Loake et al., Proc. Natl. Acad. Sci. USA 89:9230-9234 (1992); Mhiri etal., Plant Mol. Biol. 33:257-266 (1997)), antioxidant response elements(Rushmore et al., J. Biol. Chem. 266:11632-11639; Dalton et al., NucleicAcids Res. 22:5016-5023 (1994)), Sph elements (Suzuki et al., Plant Cell9:799-807 1997)), elicitor responsive elements, (Fukuda et al., PlantMol. Biol. 34:81-87 (1997); Rushton et al., EMBO J. 15:5690-5700(1996)), metal responsive elements (Stuart et al., Nature 317:828-831(1985); Westin et al., EMBO J. 7:3763-3770 (1988); Thiele et al.,Nucleic Acids Res. 20:1183-1191 (1992); Faisst et al., Nucleic AcidsRes. 20:3-26 (1992)), low temperature responsive elements, (Baker etal., Plant Mol. Biol. 24:701-713 (1994); Jiang et al., Plant Mol. Biol.30:679-684 (1996); Nordin et al., Plant Mol. Biol. 21:641-653 (1993);Zhou et al., J. Biol. Chem. 267:23515-23519 (1992)), drought responsiveelements, (Yamaguchi et al., Plant Cell 6:251-264 (1994); Wang et al.,Plant Mol. Biol. 28:605-617 (1995); Bray EA, Trends in Plant Science2:48-54 (1997)) enhancer elements for glutenin, (Colot et al., EMBO J.6:3559-3564 (1987); Thomas et al., Plant Cell 2:1171-1180 (1990); Kreiset al., Philos. Trans. R. Soc. Lond., B314:355-365 (1986)),light-independent regulatory elements, (Lagrange et al., Plant Cell9:1469-1479 (1997); Villain et al., J. Biol. Chem. 271:32593-32598(1996)), OCS enhancer elements, (Bouchez et al., EMBO J. 8:4197-4204(1989); Foley et al., Plant J. 3:669-679 (1993)), ACGT elements, (Fosteret al., FASEB J. 8:192-200 (1994); Izawa et al., Plant Cell 6:1277-1287(1994); Izawa et al., J. Mol. Biol. 230:1131-1144 (1993)), negative ciselements in plastid related genes, (Zhou et al., J. Biol. Chem.267:23515-23519 (1992); Lagrange et al., Mol. Cell Biol. 13:2614-2622(1993); Lagrange et al., Plant Cell 9:1469-1479 (1997); Zhou et al., J.Biol. Chem. 267:23515-23519 (1992)), prolamin box elements, (Forde etal., Nucleic Acids Res. 13:7327-7339 (1985); Colot et al., EMBO J.6:3559-3564 (1987); Thomas et al., Plant Cell 2:1171-1180 (1990);Thompson et al., Plant Mol. Biol. 15:755-764 (1990); Vicente et al.,Proc. Natl. Acad. Sci. USA 94:7685-7690 (1997)), elements in enhancersfrom the IgM heavy chain gene (Gillies et al., Cell 33:717-728 (1983);Whittier et al., Nucleic Acids Res. 15:2515-2535 (1987)). Examples ofpromoters include: those described in U.S. Pat. No. 6,437,217 (maizeRS81 promoter), U.S. Pat. No. 5,641,876 (rice actin promoter), U.S. Pat.No. 6,426,446 (maize RS324 promoter), U.S. Pat. No. 6,429,362 (maizePR-1 promoter), U.S. Pat. No. 6,232,526 (maize A3 promoter), U.S. Pat.No. 6,177,611 (constitutive maize promoters), U.S. Pat. Nos. 5,322,938,5,352,605, 5,359,142 and 5,530,196 (35S promoter), U.S. Pat. No.6,433,252 (maize L3 oleosin promoter, P-Zm.L3), U.S. Pat. No. 6,429,357(rice actin 2 promoter as well as a rice actin 2 intron), U.S. Pat. No.5,837,848 (root specific promoter), U.S. Pat. No. 6,294,714 (lightinducible promoters), U.S. Pat. No. 6,140,078 (salt induciblepromoters), U.S. Pat. No. 6,252,138 (pathogen inducible promoters), U.S.Pat. No. 6,175,060 (phosphorus deficiency inducible promoters), U.S.Pat. No. 6,635,806 (gama-coixin promoter, P-y.Gcx), U.S. patentapplication Ser. No. 09/757,089 (maize chloroplast aldolase promoter),and U.S. Pat. No. 8,772,466 (maize transcription factor Nuclear Factor B(NFB2)).

Suitable constitutive promoters for use in a plant host cell include,for example, the core promoter of the Rsyn7 promoter and otherconstitutive promoters disclosed in WO 1999/43838 and U.S. Pat. No.6,072,050; the core CaMV 35S promoter (Odell, et al., (1985) Nature313:810-812); rice actin (McElroy, et al., (1990) Plant Cell 2:163-171);ubiquitin (Christensen, et al., (1989) Plant Mol. Biol. 12:619-632 andChristensen, et al., (1992) Plant Mol. Biol. 18:675-689); pEMU (Last, etal., (1991) Theor. Appl. Genet. 81:581-588); MAS (Velten, et al., (1984)EMBO J. 3:2723-2730); ALS promoter (U.S. Pat. No. 5,659,026) and thelike. Other constitutive promoters include, for example, those discussedin U.S. Pat. Nos. 5,608,149; 5,608,144; 5,604,121; 5,569,597; 5,466,785;5,399,680; 5,268,463; 5,608,142 and 6,177,611. Suitable constitutivepromoters also include promoters that have strong expression in nearlyall tissues but have low expression in pollen, including but not limitedto: Banana Streak Virus (Acuminata Yunnan) promoters (BSV(AY)) disclosedin US patent U.S. Pat. No. 8,338,662; Banana Streak Virus (AcuminataVietnam) promoters (BSV(AV)) disclosed in US patent U.S. Pat. No.8,350,121; and Banana Streak Virus (Mysore) promoters (BSV(MYS))disclosed in US patent U.S. Pat. No. 8,395,022.

Depending on the desired outcome, it may be beneficial to express thegene from an inducible promoter. Of particular interest for regulatingthe expression of the nucleotide sequences of the embodiments in plantsare wound-inducible promoters. Such wound-inducible promoters, mayrespond to damage caused by insect feeding, and include potatoproteinase inhibitor (pin II) gene (Ryan, (1990) Ann. Rev. Phytopath.28:425-449; Duan, et al., (1996) Nature Biotechnology 14:494-498); wun1and wun2, U.S. Pat. No. 5,428,148; win1 and win2 (Stanford, et al.,(1989) Mol. Gen. Genet. 215:200-208); systemin (McGurl, et al., (1992)Science 225:1570-1573); WIP1 (Rohmeier, et al., (1993) Plant Mol. Biol.22:783-792; Eckelkamp, et al., (1993) FEBS Letters 323:73-76); MPI gene(Corderok, et al., (1994) Plant J. 6(2):141-150) and the like, hereinincorporated by reference.

Additionally, pathogen-inducible promoters may be employed in themethods and nucleotide constructs of the embodiments. Suchpathogen-inducible promoters include those from pathogenesis-relatedproteins (PR proteins), which are induced following infection by apathogen; e.g., PR proteins, SAR proteins, beta-1,3-glucanase,chitinase, etc. See, for example, Redolfi, et al., (1983) Neth. J. PlantPathol. 89:245-254; Uknes, et al., (1992) Plant Cell 4: 645-656 and VanLoon, (1985) Plant Mol. Virol. 4:111-116. See also, WO 1999/43819,herein incorporated by reference.

Of interest are promoters that are expressed locally at or near the siteof pathogen infection. See, for example, Marineau, et al., (1987) PlantMol. Biol. 9:335-342; Matton, et al., (1989) Molecular Plant-MicrobeInteractions 2:325-331; Somsisch, et al., (1986) Proc. Natl. Acad. Sci.USA 83:2427-2430; Somsisch, et al., (1988) Mol. Gen. Genet. 2:93-98 andYang, (1996) Proc. Natl. Acad. Sci. USA 93:14972-14977. See also, Chen,et al., (1996) Plant J. 10:955-966; Zhang, et al., (1994) Proc. Natl.Acad. Sci. USA 91:2507-2511; Warner, et al., (1993) Plant J. 3:191-201;Siebertz, et al., (1989) Plant Cell 1:961-968; U.S. Pat. No. 5,750,386(nematode-inducible) and the references cited therein. Of particularinterest is the inducible promoter for the maize PRms gene, whoseexpression is induced by the pathogen Fusarium moniliforme (see, forexample, Cordero, et al., (1992) Physiol. Mol. Plant Path. 41:189-200).

Chemical-regulated promoters can be used to modulate the expression of agene in a plant through the application of an exogenous chemicalregulator. Depending upon the objective, the promoter may be achemical-inducible promoter, where application of the chemical inducesgene expression or a chemical-repressible promoter, where application ofthe chemical represses gene expression. Chemical-inducible promoters areknown in the art and include, but are not limited to, the maize In2-2promoter, which is activated by benzenesulfonamide herbicide safeners,the maize GST promoter, which is activated by hydrophobic electrophiliccompounds that are used as pre-emergent herbicides, and the tobaccoPR-la promoter, which is activated by salicylic acid. Otherchemical-regulated promoters of interest include steroid-responsivepromoters (see, for example, the glucocorticoid-inducible promoter inSchena, et al., (1991) Proc. Natl. Acad. Sci. USA 88:10421-10425 andMcNellis, et al., (1998) Plant J. 14(2):247-257) andtetracycline-inducible and tetracycline-repressible promoters (see, forexample, Gatz, et al., (1991) Mol. Gen. Genet. 227:229-237 and U.S. Pat.Nos. 5,814,618 and 5,789,156), herein incorporated by reference.

Tissue-preferred promoters can be utilized to target enhanced PIP-72polypeptide expression within a particular plant tissue.Tissue-preferred promoters include those discussed in Yamamoto, et al.,(1997) Plant J. 12(2)255-265; Kawamata, et al., (1997) Plant CellPhysiol. 38(7):792-803; Hansen, et al., (1997) Mol. Gen Genet.254(3):337-343; Russell, et al., (1997) Transgenic Res. 6(2):157-168;Rinehart, et al., (1996) Plant Physiol. 112(3):1331-1341; Van Camp, etal., (1996) Plant Physiol. 112(2):525-535; Canevascini, et al., (1996)Plant Physiol. 112(2):513-524; Yamamoto, et al., (1994) Plant CellPhysiol. 35(5):773-778; Lam, (1994) Results Probl. Cell Differ.20:181-196; Orozco, et al., (1993) Plant Mol Biol. 23(6):1129-1138;Matsuoka, et al., (1993) Proc Natl. Acad. Sci. USA 90(20):9586-9590 andGuevara-Garcia, et al., (1993) Plant J. 4(3):495-505. Such promoters canbe modified, if necessary, for weak expression.

Leaf-preferred promoters are known in the art. See, for example,Yamamoto, et al., (1997) Plant J. 12(2):255-265; Kwon, et al., (1994)Plant Physiol. 105:357-67; Yamamoto, et al., (1994) Plant Cell Physiol.35(5):773-778; Gotor, et al., (1993) Plant J. 3:509-18; Orozco, et al.,(1993) Plant Mol. Biol. 23(6):1129-1138 and Matsuoka, et al., (1993)Proc. Natl. Acad. Sci. USA 90(20):9586-9590.

Root-preferred or root-specific promoters are known and can be selectedfrom the many available from the literature or isolated de novo fromvarious compatible species. See, for example, Hire, et al., (1992) PlantMol. Biol. 20(2):207-218 (soybean root-specific glutamine synthetasegene); Keller and Baumgartner, (1991) Plant Cell 3(10):1051-1061(root-specific control element in the GRP 1.8 gene of French bean);Sanger, et al., (1990) Plant Mol. Biol. 14(3):433-443 (root-specificpromoter of the mannopine synthase (MAS) gene of Agrobacteriumtumefaciens) and Miao, et al., (1991) Plant Cell 3(1):11-22 (full-lengthcDNA clone encoding cytosolic glutamine synthetase (GS), which isexpressed in roots and root nodules of soybean). See also, Bogusz, etal., (1990) Plant Cell 2(7):633-641, where two root-specific promotersisolated from hemoglobin genes from the nitrogen-fixing nonlegumeParasponia andersonii and the related non-nitrogen-fixing nonlegumeTrema tomentosa are described. The promoters of these genes were linkedto a β-glucuronidase reporter gene and introduced into both thenonlegume Nicotiana tabacum and the legume Lotus corniculatus, and inboth instances root-specific promoter activity was preserved. Leach andAoyagi, (1991) describe their analysis of the promoters of the highlyexpressed roIC and roID root-inducing genes of Agrobacterium rhizogenes(see, Plant Science (Limerick) 79(1):69-76). They concluded thatenhancer and tissue-preferred DNA determinants are dissociated in thosepromoters. Teeri, et al., (1989) used gene fusion to lacZ to show thatthe Agrobacterium T-DNA gene encoding octopine synthase is especiallyactive in the epidermis of the root tip and that the TR2′ gene is rootspecific in the intact plant and stimulated by wounding in leaf tissue,an especially desirable combination of characteristics for use with aninsecticidal or larvicidal gene (see, EMBO J. 8(2):343-350). The TR1′gene fused to nptII (neomycin phosphotransferase II) showed similarcharacteristics. Additional root-preferred promoters include theVfENOD-GRP3 gene promoter (Kuster, et al., (1995) Plant Mol. Biol.29(4):759-772) and roIB promoter (Capana, et al., (1994) Plant Mol.Biol. 25(4):681-691. See also, U.S. Pat. Nos. 5,837,876; 5,750,386;5,633,363; 5,459,252; 5,401,836; 5,110,732 and 5,023,179. Arabidopsisthaliana root-preferred regulatory sequences are disclosed in US PatentApplication US20130117883. Root-preferred sorghum (Sorghum bicolor) RCc3promoters are disclosed in US Patent Application US20120210463. Theroot-preferred maize promoters of US Patent Application Publication20030131377, U.S. Pat. No. 7,645,919, and 8,735,655. The rootcap-specific 1 (ZmRCP1) maize promoters of US Patent ApplicationPublication 20130025000. The root-preferred maize promoters of US PatentApplication Publication 20130312136.

“Seed-preferred” promoters include both “seed-specific” promoters (thosepromoters active during seed development such as promoters of seedstorage proteins) as well as “seed-germinating” promoters (thosepromoters active during seed germination). See, Thompson, et al., (1989)BioEssays 10:108, herein incorporated by reference. Such seed-preferredpromoters include, but are not limited to, Cim1 (cytokinin-inducedmessage); cZ19B1 (maize 19 kDa zein); and milps(myo-inositol-1-phosphate synthase) (see, U.S. Pat. No. 6,225,529,herein incorporated by reference). Gamma-zein and Glb-1 areendosperm-specific promoters. For dicots, seed-specific promotersinclude, but are not limited to, Kunitz trypsin inhibitor 3 (KTi3)(Jofuku and Goldberg, (1989) Plant Cell 1:1079-1093), bean β-phaseolin,napin, β-conglycinin, glycinin 1, soybean lectin, cruciferin, and thelike. For monocots, seed-specific promoters include, but are not limitedto, maize 15 kDa zein, 22 kDa zein, 27 kDa zein, g-zein, waxy, shrunken1, shrunken 2, globulin 1, etc. See also, WO 2000/12733, whereseed-preferred promoters from end1 and end2 genes are disclosed; hereinincorporated by reference. In dicots, seed specific promoters includebut are not limited to seed coat promoter from Arabidopsis, pBAN; andthe early seed promoters from Arabidopsis, p26, p63, and p63tr (U.S.Pat. Nos. 7,294,760 and 7,847,153). A promoter that has “preferred”expression in a particular tissue is expressed in that tissue to agreater degree than in at least one other plant tissue. Sometissue-preferred promoters show expression almost exclusively in theparticular tissue.

Where low level expression is desired, weak promoters will be used.Generally, the term “weak promoter” as used herein refers to a promoterthat drives expression of a coding sequence at a low level. By low levelexpression at levels of about 1/1000 transcripts to about 1/100,000transcripts to about 1/500,000 transcripts is intended. Alternatively,it is recognized that the term “weak promoters” also encompassespromoters that drive expression in only a few cells and not in others togive a total low level of expression. Where a promoter drives expressionat unacceptably high levels, portions of the promoter sequence can bedeleted or modified to decrease expression levels.

Such weak constitutive promoters include, for example the core promoterof the Rsyn7 promoter (WO 1999/43838 and U.S. Pat. No. 6,072,050), thecore 35S CaMV promoter, and the like. Other constitutive promotersinclude, for example, those disclosed in U.S. Pat. Nos. 5,608,149;5,608,144; 5,604,121; 5,569,597; 5,466,785; 5,399,680; 5,268,463;5,608,142 and 6,177,611, herein incorporated by reference.

The above list of promoters is not meant to be limiting. Any appropriatepromoter can be used in the embodiments.

Generally, the expression cassette will comprise a selectable markergene for the selection of transformed cells. Selectable marker genes areutilized for the selection of transformed cells or tissues. Marker genesinclude genes encoding antibiotic resistance, such as those encodingneomycin phosphotransferase II (NEO) and hygromycin phosphotransferase(HPT), as well as genes conferring resistance to herbicidal compounds,such as glufosinate ammonium, bromoxynil, imidazolinones and2,4-dichlorophenoxyacetate (2,4-D). Additional examples of suitableselectable marker genes include, but are not limited to, genes encodingresistance to chloramphenicol (Herrera Estrella, et al., (1983) EMBO J.2:987-992); methotrexate (Herrera Estrella, et al., (1983) Nature303:209-213 and Meijer, et al., (1991) Plant Mol. Biol. 16:807-820);streptomycin (Jones, et al., (1987) Mol. Gen. Genet. 210:86-91);spectinomycin (Bretagne-Sagnard, et al., (1996) Transgenic Res.5:131-137); bleomycin (Hille, et al., (1990) Plant Mol. Biol.7:171-176); sulfonamide (Guerineau, et al., (1990) Plant Mol. Biol.15:127-136); bromoxynil (Stalker, et al., (1988) Science 242:419-423);glyphosate (Shaw, et al., (1986) Science 233:478-481 and U.S. patentapplication Ser. Nos. 10/004,357 and 10/427,692); phosphinothricin(DeBlock, et al., (1987) EMBO J. 6:2513-2518). See generally, Yarranton,(1992) Curr. Opin. Biotech. 3:506-511; Christopherson, et al., (1992)Proc. Natl. Acad. Sci. USA 89:6314-6318; Yao, et al., (1992) Cell71:63-72; Reznikoff, (1992) Mol. Microbiol. 6:2419-2422; Barkley, etal., (1980) in The Operon, pp. 177-220; Hu, et al., (1987) Cell48:555-566; Brown, et al., (1987) Cell 49:603-612; Figge, et al., (1988)Cell 52:713-722; Deuschle, et al., (1989) Proc. Natl. Acad. Sci. USA86:5400-5404; Fuerst, et al., (1989) Proc. Natl. Acad. Sci. USA86:2549-2553; Deuschle, et al., (1990) Science 248:480-483; Gossen,(1993) Ph.D. Thesis, University of Heidelberg; Reines, et al., (1993)Proc. Natl. Acad. Sci. USA 90:1917-1921; Labow, et al., (1990) Mol.Cell. Biol. 10:3343-3356; Zambretti, et al., (1992) Proc. Natl. Acad.Sci. USA 89:3952-3956; Baim, et al., (1991) Proc. Natl. Acad. Sci. USA88:5072-5076; Wyborski, et al., (1991) Nucleic Acids Res. 19:4647-4653;Hillenand-Wissman, (1989) Topics Mol. Struc. Biol. 10:143-162;Degenkolb, et al., (1991) Antimicrob. Agents Chemother. 35:1591-1595;Kleinschnidt, et al., (1988) Biochemistry 27:1094-1104; Bonin, (1993)Ph.D. Thesis, University of Heidelberg; Gossen, et al., (1992) Proc.Natl. Acad. Sci. USA 89:5547-5551; Oliva, et al., (1992) Antimicrob.Agents Chemother. 36:913-919; Hlavka, et al., (1985) Handbook ofExperimental Pharmacology, Vol. 78 (Springer-Verlag, Berlin) and Gill,et al., (1988) Nature 334:721-724. Such disclosures are hereinincorporated by reference.

The above list of selectable marker genes is not meant to be limiting.Any selectable marker gene can be used in the embodiments.

Plant Transformation

The methods of the embodiments involve introducing a polypeptide orpolynucleotide into a plant. “Introducing” is as used herein meanspresenting to the plant the polynucleotide or polypeptide in such amanner that the sequence gains access to the interior of a cell of theplant. The methods of the embodiments do not depend on a particularmethod for introducing a polynucleotide or polypeptide into a plant,only that the polynucleotide or polypeptides gains access to theinterior of at least one cell of the plant. Methods for introducingpolynucleotide or polypeptides into plants are known in the artincluding, but not limited to, stable transformation methods, transienttransformation methods, and virus-mediated methods.

“Stable transformation” is as used herein means that the nucleotideconstruct introduced into a plant integrates into the genome of theplant and is capable of being inherited by the progeny thereof.“Transient transformation” as used herein means that a polynucleotide isintroduced into the plant and does not integrate into the genome of theplant or a polypeptide is introduced into a plant. “Plant” as usedherein refers to whole plants, plant organs (e.g., leaves, stems, roots,etc.), seeds, plant cells, propagules, embryos and progeny of the same.Plant cells can be differentiated or undifferentiated (e.g. callus,suspension culture cells, protoplasts, leaf cells, root cells, phloemcells and pollen).

Transformation protocols as well as protocols for introducing nucleotidesequences into plants may vary depending on the type of plant or plantcell, i.e., monocot or dicot, targeted for transformation. Suitablemethods of introducing nucleotide sequences into plant cells andsubsequent insertion into the plant genome include microinjection(Crossway, et al., (1986) Biotechniques 4:320-334), electroporation(Riggs, et al., (1986) Proc. Natl. Acad. Sci. USA 83:5602-5606),Agrobacterium-mediated transformation (U.S. Pat. Nos. 5,563,055 and5,981,840), direct gene transfer (Paszkowski, et al., (1984) EMBO J.3:2717-2722) and ballistic particle acceleration (see, for example, U.S.Pat. Nos. 4,945,050; 5,879,918; 5,886,244 and 5,932,782; Tomes, et al.,(1995) in Plant Cell, Tissue, and Organ Culture: Fundamental Methods,ed. Gamborg and Phillips, (Springer-Verlag, Berlin) and McCabe, et al.,(1988) Biotechnology 6:923-926) and Lecl transformation (WO 00/28058).For potato transformation see, Tu, et al., (1998) Plant MolecularBiology 37:829-838 and Chong, et al., (2000) Transgenic Research9:71-78. Additional transformation procedures can be found inWeissinger, et al., (1988) Ann. Rev. Genet. 22:421-477; Sanford, et al.,(1987) Particulate Science and Technology 5:27-37 (onion); Christou, etal., (1988) Plant Physiol. 87:671-674 (soybean); McCabe, et al., (1988)Bio/Technology 6:923-926 (soybean); Finer and McMullen, (1991) In VitroCell Dev. Biol. 27P:175-182 (soybean); Singh, et al., (1998) Theor.Appl. Genet. 96:319-324 (soybean); Datta, et al., (1990) Biotechnology8:736-740 (rice); Klein, et al., (1988) Proc. Natl. Acad. Sci. USA85:4305-4309 (maize); Klein, et al., (1988) Biotechnology 6:559-563(maize); U.S. Pat. Nos. 5,240,855; 5,322,783 and 5,324,646; Klein, etal., (1988) Plant Physiol. 91:440-444 (maize); Fromm, et al., (1990)Biotechnology 8:833-839 (maize); Hooykaas-Van Slogteren, et al., (1984)Nature (London) 311:763-764; U.S. Pat. No. 5,736,369 (cereals);Bytebier, et al., (1987) Proc. Natl. Acad. Sci. USA 84:5345-5349(Liliaceae); De Wet, et al., (1985) in The Experimental Manipulation ofOvule Tissues, ed. Chapman, et al., (Longman, New York), pp. 197-209(pollen); Kaeppler, et al., (1990) Plant Cell Reports 9:415-418 andKaeppler, et al., (1992) Theor. Appl. Genet. 84:560-566(whisker-mediated transformation); D′Halluin, et al., (1992) Plant Cell4:1495-1505 (electroporation); Li, et al., (1993) Plant Cell Reports12:250-255 and Christou and Ford, (1995) Annals of Botany 75:407-413(rice); Osjoda, et al., (1996) Nature Biotechnology 14:745-750 (maizevia Agrobacterium tumefaciens); all of which are herein incorporated byreference.

In specific embodiments, the sequences of the embodiments can beprovided to a plant using a variety of transient transformation methods.Such transient transformation methods include, but are not limited to,the introduction of the PIP-72 polypeptide or variants and fragmentsthereof and a polynucleotide encoding a silencing element directly intothe plant or the introduction of the PIP-72 polypeptide transcript and asilencing element into the plant. Such methods include, for example,microinjection or particle bombardment. See, for example, Crossway, etal., (1986) Mol Gen. Genet. 202:179-185; Nomura, et al., (1986) PlantSci. 44:53-58; Hepler, et al., (1994) Proc. Natl. Acad. Sci.91:2176-2180 and Hush, et al., (1994) The Journal of Cell Science107:775-784, all of which are herein incorporated by reference.Alternatively, the PIP-72 polypeptide polynucleotide can be transientlytransformed into the plant using techniques known in the art. Suchtechniques include viral vector system and the precipitation of thepolynucleotide in a manner that precludes subsequent release of the DNA.Thus, transcription from the particle-bound DNA can occur, but thefrequency with which it is released to become integrated into the genomeis greatly reduced. Such methods include the use of particles coatedwith polyethylimine (PEI; Sigma #P3143).

Methods are known in the art for the targeted insertion of apolynucleotide at a specific location in the plant genome. In oneembodiment, the insertion of the polynucleotide at a desired genomiclocation is achieved using a site-specific recombination system. See,for example, WO 1999/25821, WO 1999/25854, WO 1999/25840, WO 1999/25855and WO 1999/25853, all of which are herein incorporated by reference.Briefly, the polynucleotide of the embodiments can be contained intransfer cassette flanked by two non-identical recombination sites. Thetransfer cassette is introduced into a plant have stably incorporatedinto its genome a target site which is flanked by two non-identicalrecombination sites that correspond to the sites of the transfercassette. An appropriate recombinase is provided and the transfercassette is integrated at the target site. The polynucleotide ofinterest is thereby integrated at a specific chromosomal position in theplant genome.

Plant transformation vectors may be comprised of one or more DNA vectorsneeded for achieving plant transformation. For example, it is a commonpractice in the art to utilize plant transformation vectors that arecomprised of more than one contiguous DNA segment. These vectors areoften referred to in the art as “binary vectors”. Binary vectors as wellas vectors with helper plasmids are most often used forAgrobacterium-mediated transformation, where the size and complexity ofDNA segments needed to achieve efficient transformation is quite large,and it is advantageous to separate functions onto separate DNAmolecules. Binary vectors typically contain a plasmid vector thatcontains the cis-acting sequences required for T-DNA transfer (such asleft border and right border), a selectable marker that is engineered tobe capable of expression in a plant cell, and a “gene of interest” (agene engineered to be capable of expression in a plant cell for whichgeneration of transgenic plants is desired). Also present on thisplasmid vector are sequences required for bacterial replication. Thecis-acting sequences are arranged in a fashion to allow efficienttransfer into plant cells and expression therein. For example, theselectable marker gene and the pesticidal gene are located between theleft and right borders. Often a second plasmid vector contains thetrans-acting factors that mediate T-DNA transfer from Agrobacterium toplant cells. This plasmid often contains the virulence functions (Virgenes) that allow infection of plant cells by Agrobacterium, andtransfer of DNA by cleavage at border sequences and vir-mediated DNAtransfer, as is understood in the art (Hellens and Mullineaux, (2000)Trends in Plant Science 5:446-451). Several types of Agrobacteriumstrains (e.g. LBA4404, GV3101, EHA101, EHA105, etc.) can be used forplant transformation. The second plasmid vector is not necessary fortransforming the plants by other methods such as microprojection,microinjection, electroporation, polyethylene glycol, etc.

In general, plant transformation methods involve transferringheterologous DNA into target plant cells (e.g., immature or matureembryos, suspension cultures, undifferentiated callus, protoplasts,etc.), followed by applying a maximum threshold level of appropriateselection (depending on the selectable marker gene) to recover thetransformed plant cells from a group of untransformed cell mass.Following integration of heterologous foreign DNA into plant cells, onethen applies a maximum threshold level of appropriate selection in themedium to kill the untransformed cells and separate and proliferate theputatively transformed cells that survive from this selection treatmentby transferring regularly to a fresh medium. By continuous passage andchallenge with appropriate selection, one identifies and proliferatesthe cells that are transformed with the plasmid vector. Molecular andbiochemical methods can then be used to confirm the presence of theintegrated heterologous gene of interest into the genome of thetransgenic plant.

Explants are typically transferred to a fresh supply of the same mediumand cultured routinely. Subsequently, the transformed cells aredifferentiated into shoots after placing on regeneration mediumsupplemented with a maximum threshold level of selecting agent. Theshoots are then transferred to a selective rooting medium for recoveringrooted shoot or plantlet. The transgenic plantlet then grows into amature plant and produces fertile seeds (e.g., Hiei, et al., (1994) ThePlant Journal 6:271-282; Ishida, et al., (1996) Nature Biotechnology14:745-750). Explants are typically transferred to a fresh supply of thesame medium and cultured routinely. A general description of thetechniques and methods for generating transgenic plants are found inAyres and Park, (1994) Critical Reviews in Plant Science 13:219-239 andBommineni and Jauhar, (1997) Maydica 42:107-120. Since the transformedmaterial contains many cells; both transformed and non-transformed cellsare present in any piece of subjected target callus or tissue or groupof cells. The ability to kill non-transformed cells and allowtransformed cells to proliferate results in transformed plant cultures.Often, the ability to remove non-transformed cells is a limitation torapid recovery of transformed plant cells and successful generation oftransgenic plants.

The cells that have been transformed may be grown into plants inaccordance with conventional ways. See, for example, McCormick, et al.,(1986) Plant Cell Reports 5:81-84. These plants may then be grown, andeither pollinated with the same transformed strain or different strains,and the resulting hybrid having constitutive or inducible expression ofthe desired phenotypic characteristic identified. Two or moregenerations may be grown to ensure that expression of the desiredphenotypic characteristic is stably maintained and inherited and thenseeds harvested to ensure that expression of the desired phenotypiccharacteristic has been achieved.

The nucleotide sequences of the embodiments may be provided to the plantby contacting the plant with a virus or viral nucleic acids. Generally,such methods involve incorporating the nucleotide construct of interestwithin a viral DNA or RNA molecule. It is recognized that therecombinant proteins of the embodiments may be initially synthesized aspart of a viral polyprotein, which later may be processed by proteolysisin vivo or in vitro to produce the desired PIP-72 polypeptide. It isalso recognized that such a viral polyprotein, comprising at least aportion of the amino acid sequence of a PIP-72 polypeptide of theembodiments, may have the desired pesticidal activity. Such viralpolyproteins and the nucleotide sequences that encode for them areencompassed by the embodiments. Methods for providing plants withnucleotide constructs and producing the encoded proteins in the plants,which involve viral DNA or RNA molecules are known in the art. See, forexample, U.S. Pat. Nos. 5,889,191; 5,889,190; 5,866,785; 5,589,367 and5,316,931; herein incorporated by reference.

Methods for transformation of chloroplasts are known in the art. See,for example, Svab, et al., (1990) Proc. Natl. Acad. Sci. USA87:8526-8530; Svab and Maliga, (1993) Proc. Natl. Acad. Sci. USA90:913-917; Svab and Maliga, (1993) EMBO J. 12:601-606. The methodrelies on particle gun delivery of DNA containing a selectable markerand targeting of the DNA to the plastid genome through homologousrecombination. Additionally, plastid transformation can be accomplishedby transactivation of a silent plastid-borne transgene bytissue-preferred expression of a nuclear-encoded and plastid-directedRNA polymerase. Such a system has been reported in McBride, et al.,(1994) Proc. Natl. Acad. Sci. USA 91:7301-7305.

The embodiments further relate to plant-propagating material of atransformed plant of the embodiments including, but not limited to,seeds, tubers, corms, bulbs, leaves and cuttings of roots and shoots.

The embodiments may be used for transformation of any plant species,including, but not limited to, monocots and dicots. Examples of plantsof interest include, but are not limited to, corn (Zea mays), Brassicasp. (e.g., B. napus, B. rapa, B. juncea), particularly those Brassicaspecies useful as sources of seed oil, alfalfa (Medicago sativa), rice(Oryza sativa), rye (Secale cereale), sorghum (Sorghum bicolor, Sorghumvulgare), millet (e.g., pearl millet (Pennisetum glaucum), proso millet(Panicum miliaceum), foxtail millet (Setaria italica), finger millet(Eleusine coracana)), sunflower (Helianthus annuus), safflower(Carthamus tinctorius), wheat (Triticum aestivum), soybean (Glycinemax), tobacco (Nicotiana tabacum), potato (Solanum tuberosum), peanuts(Arachis hypogaea), cotton (Gossypium barbadense, Gossypium hirsutum),sweet potato (Ipomoea batatus), cassava (Manihot esculenta), coffee(Coffea spp.), coconut (Cocos nucifera), pineapple (Ananas comosus),citrus trees (Citrus spp.), cocoa (Theobroma cacao), tea (Camelliasinensis), banana (Musa spp.), avocado (Persea americana), fig (Ficuscasica), guava (Psidium guajava), mango (Mangifera indica), olive (Oleaeuropaea), papaya (Carica papaya), cashew (Anacardium occidentale),macadamia (Macadamia integrifolia), almond (Prunus amygdalus), sugarbeets (Beta vulgaris), sugarcane (Saccharum spp.), oats, barley,vegetables ornamentals, and conifers.

Vegetables include tomatoes (Lycopersicon esculentum), lettuce (e.g.,Lactuca sativa), green beans (Phaseolus vulgaris), lima beans (Phaseoluslimensis), peas (Lathyrus spp.), and members of the genus Cucumis suchas cucumber (C. sativus), cantaloupe (C. cantalupensis), and musk melon(C. melo). Ornamentals include azalea (Rhododendron spp.), hydrangea(Macrophylla hydrangea), hibiscus (Hibiscus rosasanensis), roses (Rosaspp.), tulips (Tulipa spp.), daffodils (Narcissus spp.), petunias(Petunia hybrida), carnation (Dianthus caryophyllus), poinsettia(Euphorbia pulcherrima), and chrysanthemum. Conifers that may beemployed in practicing the embodiments include, for example, pines suchas loblolly pine (Pinus taeda), slash pine (Pinus elliotii), ponderosapine (Pinus ponderosa), lodgepole pine (Pinus contorta), and Montereypine (Pinus radiata); Douglas-fir (Pseudotsuga menziesii); Westernhemlock (Tsuga canadensis); Sitka spruce (Picea glauca); redwood(Sequoia sempervirens); true firs such as silver fir (Abies amabilis)and balsam fir (Abies balsamea); and cedars such as Western red cedar(Thuja plicata) and Alaska yellow-cedar (Chamaecyparis nootkatensis).Plants of the embodiments include crop plants (for example, corn,alfalfa, sunflower, Brassica, soybean, cotton, safflower, peanut,sorghum, wheat, millet, tobacco, etc.), such as corn and soybean plants.

Turf grasses include, but are not limited to: annual bluegrass (Poaannus); annual ryegrass (Lolium multiflorum); Canada bluegrass (Poacompressa); Chewing's fescue (Festuca rubra); colonial bentgrass(Agrostis tenuis); creeping bentgrass (Agrostis palustris); crestedwheatgrass (Agropyron desertorum); fairway wheatgrass (Agropyroncristatum); hard fescue (Festuca longifolia); Kentucky bluegrass (Poapratensis); orchardgrass (Dactylis glomerata); perennial ryegrass(Lolium perenne); red fescue (Festuca rubra); redtop (Agrostis alba);rough bluegrass (Poa trivialis); sheep fescue (Festuca ovini); smoothbromegrass (Bromus inermis); tall fescue (Festuca arundinacea); timothy(Phleum pratense); velvet bentgrass (Agrostis canina); weepingalkaligrass (Puccinellia distans); western wheatgrass (Agropyronsmithii); Bermuda grass (Cynodon spp.); St. Augustine grass(Stenotaphrum secundatum); zoysia grass (Zoysia spp.); Bahia grass(Paspalum notatum); carpet grass (Axonopus affinis); centipede grass(Eremochloa ophiuroides); kikuyu grass (Pennisetum clandesinum);seashore paspalum (Paspalum vaginatum); blue gramma (Boutelouagracilis); buffalo grass (Buchloe dactyloids); sideoats gramma(Bouteloua curtipendula).

Plants of interest include grain plants that provide seeds of interest,oil-seed plants, and leguminous plants. Seeds of interest include grainseeds, such as corn, wheat, barley, rice, sorghum, rye, millet, etc.Oil-seed plants include cotton, soybean, safflower, sunflower, Brassica,maize, alfalfa, palm, coconut, flax, castor, olive, etc. Leguminousplants include beans and peas. Beans include guar, locust bean,fenugreek, soybean, garden beans, cowpea, mung bean, lima bean, favabean, lentils, chickpea, etc.

Evaluation of Plant Transformation

Following introduction of heterologous foreign DNA into plant cells, thetransformation or integration of heterologous gene in the plant genomeis confirmed by various methods such as analysis of nucleic acids,proteins and metabolites associated with the integrated gene.

PCR analysis is a rapid method to screen transformed cells, tissue orshoots for the presence of incorporated gene at the earlier stage beforetransplanting into the soil (Sambrook and Russell, (2001) MolecularCloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press, ColdSpring Harbor, N.Y.). PCR is carried out using oligonucleotide primersspecific to the gene of interest or Agrobacterium vector background,etc.

Plant transformation may be confirmed by Southern blot analysis ofgenomic DNA (Sambrook and Russell, (2001) supra). In general, total DNAis extracted from the transformant, digested with appropriaterestriction enzymes, fractionated in an agarose gel and transferred to anitrocellulose or nylon membrane. The membrane or “blot” is then probedwith, for example, radiolabeled 32P target DNA fragment to confirm theintegration of introduced gene into the plant genome according tostandard techniques (Sambrook and Russell, (2001) supra).

In Northern blot analysis, RNA is isolated from specific tissues oftransformant, fractionated in a formaldehyde agarose gel, and blottedonto a nylon filter according to standard procedures that are routinelyused in the art (Sambrook and Russell, (2001) supra). Expression of RNAencoded by the pesticidal gene is then tested by hybridizing the filterto a radioactive probe derived from a pesticidal gene, by methods knownin the art (Sambrook and Russell, (2001) supra).

Western blot, biochemical assays and the like may be carried out on thetransgenic plants to confirm the presence of protein encoded by thepesticidal gene by standard procedures (Sambrook and Russell, 2001,supra) using antibodies that bind to one or more epitopes present on thePIP-72 polypeptide.

Stacking of Traits of PIP-72 and Silencing Elements in Transgenic Plant

Transgenic plants may comprise a stack of one or more insecticidalpolynucleotides disclosed herein with one or more additionalpolynucleotides resulting in the production or suppression of multipleinsecticidal polypeptide sequences. Transgenic plants comprising stacksof polynucleotide sequences can be obtained by either or both oftraditional breeding methods or through genetic engineering methods.These methods include, but are not limited to, breeding individual lineseach comprising a polynucleotide of interest, transforming a transgenicplant comprising a gene or silencing element disclosed herein with asubsequent gene or silencing element and co-transformation of genesand/or silencing elements into a single plant cell. As used herein, theterm “stacked” includes having the multiple traits present in the sameplant (i.e., both traits are incorporated into the nuclear genome, onetrait is incorporated into the nuclear genome and one trait isincorporated into the genome of a plastid or both traits areincorporated into the genome of a plastid). In one non-limiting example,“stacked traits” comprise a molecular stack where the sequences arephysically adjacent to each other. A trait, as used herein, refers tothe phenotype derived from a particular sequence or groups of sequences.Co-transformation of genes can be carried out using singletransformation vectors comprising multiple genes or genes carriedseparately on multiple vectors. If the sequences are stacked bygenetically transforming the plants, the polynucleotide sequences ofinterest can be combined at any time and in any order. The traits can beintroduced simultaneously in a co-transformation protocol with thepolynucleotides of interest provided by any combination oftransformation cassettes. For example, if two sequences will beintroduced, the two sequences can be contained in separatetransformation cassettes (trans) or contained on the same transformationcassette (cis). Expression of the sequences can be driven by the samepromoter or by different promoters. In certain cases, it may bedesirable to introduce a transformation cassette that will suppress theexpression of the polynucleotide of interest. This may be combined withany combination of other suppression cassettes or overexpressioncassettes to generate the desired combination of traits in the plant. Itis further recognized that polynucleotide sequences can be stacked at adesired genomic location using a site-specific recombination system.See, for example, WO 1999/25821, WO 1999/25854, WO 1999/25840, WO1999/25855 and WO 1999/25853, all of which are herein incorporated byreference.

In some embodiments one or more polynucleotide encoding the polypeptidesof the PIP-72 polypeptides or fragments or variants thereof may bestacked with one or more polynucleotides encoding one or morepolypeptides having insecticidal activity or agronomic traits as setforth supra and optionally may further include one or morepolynucleotides providing for gene silencing of one or more targetpolynucleotides as discussed infra.

In some embodiments polynucleotides encoding one or more of the PIP-72polypeptides disclosed herein are stacked with one or morepolynucleotides encoding pesticidal proteins disclosed herein.

In one embodiment, polynucleotides encoding one or more of the PIP-72polypeptides disclosed herein are stacked with one or morepolynucleotides encoding PIP-47 polypeptides of W02015/023846, which isincorporated by reference in its entirety.

Gene Silencing

In some embodiments the stacked trait may be in the form of silencing ofone or more polynucleotides of interest resulting in suppression of oneor more target pest polypeptides. In some embodiments the silencing isachieved through the use of a silencing element.

In some embodiments the polynucleotides encoding the PIP-72 polypeptidesdisclosed herein are stacked with one or more silencing elements havinginsecticidal activity.

In some embodiments the polynucleotides encoding the PIP-72 polypeptidesdisclosed herein are stacked with one or more polynucleotides encodingsilencing elements targeting RyanR (SEQ ID NO: 992), HP2 SEQ ID NO:994), or RPS10 (SEQ ID NO: 995). In one embodiment, the polynucleotidesencoding the PIP-72 polypeptides disclosed herein are stacked withpolynucleotides encoding a silencing element disclosed in US PatentApplication Publication No. US US2014/0275208 or US2015/0257389. In oneembodiment, the polynucleotides encoding the PIP-72 polypeptidesdisclosed herein are stacked with polynucleotides encoding a silencingelement comprising any one of SEQ ID NOs: 982-991, 993, or SEQ ID NOs:561-572 of US Patent Application Publication No. US2014/0275208 andUS2015/0257389.

In some embodiments the polynucleotides encoding the PIP-72 polypeptidesand polynucleotides encoding silencing elements disclosed herein arestacked with one or more additional insect resistance traits.

In some embodiments the polynucleotides encoding the PIP-72 polypeptidesand polynucleotides encoding silencing elements disclosed herein are tobe stacked with one or more additional insect resistance traits can bestacked with one or more additional input traits (e.g., herbicideresistance, fungal resistance, virus resistance, stress tolerance,disease resistance, male sterility, stalk strength, and the like) oroutput traits (e.g., increased yield, modified starches, improved oilprofile, balanced amino acids, high lysine or methionine, increaseddigestibility, improved fiber quality, drought resistance, and thelike). Thus, the polynucleotide embodiments can be used to provide acomplete agronomic package of improved crop quality with the ability toflexibly and cost effectively control any number of agronomic pests.

Some embodiments relate to down-regulation of expression of target genesin insect pest species by interfering ribonucleic acid (RNA) molecules.

Silencing elements that may be stacked with one or more PIP-72polynucleotides includes the following: silencing elements of thevacuolar ATPase H subunit (US Patent Application Publication2012/0198586; insect ribosomal protein such as the ribosomal protein L19(PCT publication 2012/0198586), the ribosomal protein L40 or theribosomal protein S27A; an insect proteasome subunit such as the Rpn6protein, the Pros 25, the Rpn2 protein, the proteasome beta 1 subunitprotein or the Pros beta 2 protein; an insect β-coatomer of the COPIvesicle, the γ-coatomer of the COPI vesicle, the β′-coatomer protein orthe ζ-coatomer of the COPI vesicle; an insect Tetraspanine 2 A proteinwhich is a putative transmembrane domain protein; an insect proteinbelonging to the actin family such as Actin 5C; an insect ubiquitin-5Eprotein; an insect Sec23 protein which is a GTPase activator involved inintracellular protein transport; an insect crinkled protein which is anunconventional myosin which is involved in motor activity; an insectcrooked neck protein which is involved in the regulation of nuclearalternative mRNA splicing; an insect vacuolar H+-ATPase G-subunitprotein and an insect Tbp-1 such as Tat-binding protein. PCT publicationWO 2007/035650 describes silencing elements directed to Snf7; US PatentApplication publication 2011/0054007 describes polynucleotide silencingelements targeting RPS10; US Patent Application publicationUS2015/0257389 describes polynucleotide silencing elements targetingRyanR and PAT3; US Patent Application Publication 2012/0164205 describessilencing elements directed to a Chd3 Homologous Sequence, aBeta-Tubulin Homologous Sequence, a 40 kDa V-ATPase Homologous Sequence,a EF1α Homologous Sequence, a 26S Proteosome Subunit p28 HomologousSequence, a Juvenile Hormone Epoxide Hydrolase Homologous Sequence, aSwelling Dependent Chloride Channel Protein Homologous Sequence, aGlucose-6-Phosphate 1-Dehydrogenase Protein Homologous Sequence, anAct42A Protein Homologous Sequence, a ADP-Ribosylation Factor 1Homologous Sequence, a Transcription Factor IIB Protein HomologousSequence, a Chitinase Homologous Sequences, a Ubiquitin ConjugatingEnzyme Homologous Sequence, a Glyceraldehyde-3-Phosphate DehydrogenaseHomologous Sequence, an Ubiquitin B Homologous Sequence, a JuvenileHormone Esterase Homolog, and an Alpha Tubuliln Homologous Sequence.

Pesticidal and Insecticidal Activity

“Pest” includes but is not limited to, insects, fungi, bacteria,nematodes, mites, ticks and the like. Insect pests include insectsselected from the orders Coleoptera, Diptera, Hymenoptera, Lepidoptera,Mallophaga, Homoptera, Hemiptera Orthroptera, Thysanoptera, Dermaptera,Isoptera, Anoplura, Siphonaptera, Trichoptera, etc., particularlyLepidoptera and Coleoptera.

Those skilled in the art will recognize that not all compounds areequally effective against all pests. Compounds of the embodimentsdisplay activity against insect pests, which may include economicallyimportant agronomic, forest, greenhouse, nursery ornamentals, food andfiber, public and animal health, domestic and commercial structure,household and stored product pests.

Larvae of the order Lepidoptera include, but are not limited to,armyworms, cutworms, loopers and heliothines in the family NoctuidaeSpodoptera frugiperda J E Smith (fall armyworm); S. exigua Hübner (beetarmyworm); S. litura Fabricius (tobacco cutworm, cluster caterpillar);Mamestra configurata Walker (bertha armyworm); M. brassicae Linnaeus(cabbage moth); Agrotis ipsilon Hufnagel (black cutworm); A. orthogoniaMorrison (western cutworm); A. subterranea Fabricius (granulatecutworm); Alabama argillacea Hübner (cotton leaf worm); Trichoplusia niHübner (cabbage looper); Pseudoplusia includens Walker (soybean looper);Anticarsia gemmatalis Hübner (velvetbean caterpillar); Hypena scabraFabricius (green cloverworm); Heliothis virescens Fabricius (tobaccobudworm); Pseudaletia unipuncta Haworth (armyworm); Athetis mindaraBarnes and Mcdunnough (rough skinned cutworm); Euxoa messoria Harris(darksided cutworm); Earias insulana Boisduval (spiny bollworm); E.vittella Fabricius (spotted bollworm); Helicoverpa armigera Hübner(American bollworm); H. zea Boddie (corn earworm or cotton bollworm);Melanchra picta Harris (zebra caterpillar); Egira (Xylomyges) curialisGrote (citrus cutworm); borers, casebearers, webworms, coneworms, andskeletonizers from the family Pyralidae Ostrinia nubilalis Hübner(European corn borer); Amyelois transitella Walker (naval orangeworm);Anagasta kuehniella Zeller (Mediterranean flour moth); Cadra cautellaWalker (almond moth); Chilo suppressalis Walker (rice stem borer); C.partellus, (sorghum borer); Corcyra cephalonica Stainton (rice moth);Crambus caliginosellus Clemens (corn root webworm); C. teterrellusZincken (bluegrass webworm); Cnaphalocrocis medinalis Guenée (rice leafroller); Desmia funeralis Hübner (grape leaffolder); Diaphania hyalinataLinnaeus (melon worm); D. nitidalis Stoll (pickleworm); Diatraeagrandiosella Dyar (southwestern corn borer), D. saccharalis Fabricius(surgarcane borer); Eoreuma loftini Dyar (Mexican rice borer); Ephestiaelutella Hübner (tobacco (cacao) moth); Galleria mellonella Linnaeus(greater wax moth); Herpetogramma licarsisalis Walker (sod webworm);Homoeosoma electellum Hulst (sunflower moth); Elasmopalpus lignosellusZeller (lesser cornstalk borer); Achroia grisella Fabricius (lesser waxmoth); Loxostege sticticalis Linnaeus (beet webworm); Orthaga thyrisalisWalker (tea tree web moth); Maruca testulalis Geyer (bean pod borer);Plodia interpunctella Hübner (Indian meal moth); Scirpophaga incertulasWalker (yellow stem borer); Udea rubigalis Guenée (celery leaftier); andleafrollers, budworms, seed worms and fruit worms in the familyTortricidae Acleris gloverana Walsingham (Western blackheaded budworm);A. variana Fernald (Eastern blackheaded budworm); Archips argyrospilaWalker (fruit tree leaf roller); A. rosana Linnaeus (European leafroller); and other Archips species, Adoxophyes orana Fischer vonRösslerstam (summer fruit tortrix moth); Cochylis hospes Walsingham(banded sunflower moth); Cydia latiferreana Walsingham (filbertworm); C.pomonella Linnaeus (coding moth); Platynota flavedana Clemens(variegated leafroller); P. stultana Walsingham (omnivorous leafroller);Lobesia botrana Denis & Schiffermüller (European grape vine moth);Spilonota ocellana Denis & Schiffermüller (eyespotted bud moth);Endopiza viteana Clemens (grape berry moth); Eupoecilia ambiguellaHübner (vine moth); Bonagota salubricola Meyrick (Brazilian appleleafroller); Grapholita molesta Busck (oriental fruit moth); Suleimahelianthana Riley (sunflower bud moth); Argyrotaenia spp.; Choristoneuraspp.

Selected other agronomic pests in the order Lepidoptera include, but arenot limited to, Alsophila pometaria Harris (fall cankerworm); Anarsialineatella Zeller (peach twig borer); Anisota senatoria J. E. Smith(orange striped oakworm); Antheraea pernyi Guérin-Méneville (Chinese OakTussah Moth); Bombyx mori Linnaeus (Silkworm); Bucculatrix thurberiellaBusck (cotton leaf perforator); Collas eurytheme Boisduval (alfalfacaterpillar); Datana integerrima Grote & Robinson (walnut caterpillar);Dendrolimus sibiricus Tschetwerikov (Siberian silk moth), Ennomossubsignaria Hübner (elm spanworm); Erannis tiliaria Harris (lindenlooper); Euproctis chrysorrhoea Linnaeus (browntail moth); Harrisinaamericana Guérin-Méneville (grapeleaf skeletonizer); Hemileuca oliviaeCockrell (range caterpillar); Hyphantria cunea Drury (fall webworm);Keiferia lycopersicella Walsingham (tomato pinworm); Lambdinafiscellaria fiscellaria Hulst (Eastern hemlock looper); L. fiscellarialugubrosa Hulst (Western hemlock looper); Leucoma salicis Linnaeus(satin moth); Lymantria dispar Linnaeus (gypsy moth); Manducaquinquemaculata Haworth (five spotted hawk moth, tomato hornworm); M.sexta Haworth (tomato hornworm, tobacco hornworm); Operophtera brumataLinnaeus (winter moth); Paleacrita vemata Peck (spring cankerworm);Papilio cresphontes Cramer (giant swallowtail orange dog); Phryganidiacalifornica Packard (California oakworm); Phyllocnistis citrellaStainton (citrus leafminer); Phyllonorycter blancardella Fabricius(spotted tentiform leafminer); Pieris brassicae Linnaeus (large whitebutterfly); P. rapae Linnaeus (small white butterfly); P. napi Linnaeus(green veined white butterfly); Platyptilia carduidactyla Riley(artichoke plume moth); Plutella xylostella Linnaeus (diamondback moth);Pectinophora gossypiella Saunders (pink bollworm); Pontia protodiceBoisduval and Leconte (Southern cabbageworm); Sabulodes aegrotata Guenée(omnivorous looper); Schizura concinna J. E. Smith (red humpedcaterpillar); Sitotroga cerealella Olivier (Angoumois grain moth);Thaumetopoea pityocampa Schiffermuller (pine processionary caterpillar);Tineola bisselliella Hummel (webbing clothesmoth); Tuta absoluta Meyrick(tomato leafminer); Yponomeuta padella Linnaeus (ermine moth); Heliothissubflexa Guenée; Malacosoma spp. and Orgyia spp.

Of interest are larvae and adults of the order Coleoptera includingweevils from the families Anthribidae, Bruchidae and Curculionidae(including, but not limited to: Anthonomus grandis Boheman (bollweevil); Lissorhoptrus oryzophilus Kuschel (rice water weevil);Sitophilus granarius Linnaeus (granary weevil); S. oryzae Linnaeus (riceweevil); Hypera punctata Fabricius (clover leaf weevil);Cylindrocopturus adspersus LeConte (sunflower stem weevil); Smicronyxfulvus LeConte (red sunflower seed weevil); S. sordidus LeConte (graysunflower seed weevil); Sphenophorus maidis Chittenden (maize billbug));flea beetles, cucumber beetles, rootworms, leaf beetles, potato beetlesand leafminers in the family Chrysomelidae (including, but not limitedto: Leptinotarsa decemlineata Say (Colorado potato beetle); Diabroticavirgifera virgifera LeConte (western corn rootworm); D. barberi Smithand Lawrence (northern corn rootworm); D. undecimpunctata howardi Barber(southern corn rootworm); Chaetocnema pulicaria Melsheimer (corn fleabeetle); Phyllotreta cruciferae Goeze (Crucifer flea beetle);Phyllotreta striolata (stripped flea beetle); Colaspis brunnea Fabricius(grape colaspis); Oulema melanopus Linnaeus (cereal leaf beetle);Zygogramma exclamationis Fabricius (sunflower beetle)); beetles from thefamily Coccinellidae (including, but not limited to: Epilachnavarivestis Mulsant (Mexican bean beetle)); chafers and other beetlesfrom the family Scarabaeidae (including, but not limited to: Popilliajaponica Newman (Japanese beetle); Cyclocephala borealis Arrow (northernmasked chafer, white grub); C. immaculata Olivier (southern maskedchafer, white grub); Rhizotrogus majalis Razoumowsky (European chafer);Phyllophaga crinita Burmeister (white grub); Ligyrus gibbosus De Geer(carrot beetle)); carpet beetles from the family Dermestidae; wirewormsfrom the family Elateridae, Eleodes spp., Melanotus spp.; Conoderusspp.; Limonius spp.; Agriotes spp.; Ctenicera spp.; Aeolus spp.; barkbeetles from the family Scolytidae and beetles from the familyTenebrionidae.

Adults and immatures of the order Diptera are of interest, includingleafminers Agromyza parvicomis Loew (corn blotch leafminer); midges(including, but not limited to: Contarinia sorghicola Coquillett(sorghum midge); Mayetiola destructor Say (Hessian fly); Sitodiplosismosellana Géhin (wheat midge); Neolasioptera murtfeldtiana Felt,(sunflower seed midge)); fruit flies (Tephritidae), Oscinella fritLinnaeus (fruit flies); maggots (including, but not limited to: Deliaplatura Meigen (seedcorn maggot); D. coarctata Fallen (wheat bulb fly)and other Delia spp., Meromyza americana Fitch (wheat stem maggot);Musca domestica Linnaeus (house flies); Fannia canicularis Linnaeus, F.femoralis Stein (lesser house flies); Stomoxys calcitrans Linnaeus(stable flies)); face flies, horn flies, blow flies, Chrysomya spp.;Phormia spp. and other muscoid fly pests, horse flies Tabanus spp.; botflies Gastrophilus spp.; Oestrus spp.; cattle grubs Hypoderma spp.; deerflies Chrysops spp.; Melophagus ovinus Linnaeus (keds) and otherBrachycera, mosquitoes Aedes spp.; Anopheles spp.; Culex spp.; blackflies Prosimulium spp.; Simulium spp.; biting midges, sand flies,sciarids, and other Nematocera.

Included as insects of interest are adults and nymphs of the ordersHemiptera and Homoptera such as, but not limited to, adelgids from thefamily Adelgidae, plant bugs from the family Miridae, cicadas from thefamily Cicadidae, leafhoppers, Empoasca spp.; from the familyCicadellidae, planthoppers from the families Cixiidae, Flatidae,Fulgoroidea, lssidae and Delphacidae, treehoppers from the familyMembracidae, psyllids from the family Psyllidae, whiteflies from thefamily Aleyrodidae, aphids from the family Aphididae, phylloxera fromthe family Phylloxeridae, mealybugs from the family Pseudococcidae,scales from the families Asterolecanidae, Coccidae, Dactylopiidae,Diaspididae, Eriococcidae Ortheziidae, Phoenicococcidae andMargarodidae, lace bugs from the family Tingidae, stink bugs from thefamily Pentatomidae, cinch bugs, Blissus spp.; and other seed bugs fromthe family Lygaeidae, spittlebugs from the family Cercopidae squash bugsfrom the family Coreidae and red bugs and cotton stainers from thefamily Pyrrhocoridae.

Agronomically important members from the order Homoptera furtherinclude, but are not limited to: Acyrthisiphon pisum Harris (pea aphid);Aphis craccivora Koch (cowpea aphid); A. fabae Scopoli (black beanaphid); A. gossypii Glover (cotton aphid, melon aphid); A. maidiradicisForbes (corn root aphid); A. pomi De Geer (apple aphid); A. spiraecolaPatch (spirea aphid); Aulacorthum solani Kaltenbach (foxglove aphid);Chaetosiphon fragaefolii Cockerell (strawberry aphid); Diuraphis noxiaKurdjumov/Mordvilko (Russian wheat aphid); Dysaphis plantagineaPaaserini (rosy apple aphid); Eriosoma lanigerum Hausmann (woolly appleaphid); Brevicoryne brassicae Linnaeus (cabbage aphid); Hyalopteruspruni Geoffroy (mealy plum aphid); Lipaphis erysimi Kaltenbach (turnipaphid); Metopolophium dirrhodum Walker (cereal aphid); Macrosiphumeuphorbiae Thomas (potato aphid); Myzus persicae Sulzer (peach-potatoaphid, green peach aphid); Nasonovia ribisnigri Mosley (lettuce aphid);Pemphigus spp. (root aphids and gall aphids); Rhopalosiphum maidis Fitch(corn leaf aphid); R. padi Linnaeus (bird cherry-oat aphid); Schizaphisgraminum Rondani (greenbug); Sipha flava Forbes (yellow sugarcaneaphid); Sitobion avenae Fabricius (English grain aphid); Therioaphismaculata Buckton (spotted alfalfa aphid); Toxoptera aurantii Boyer deFonscolombe (black citrus aphid) and T. citricida Kirkaldy (brown citrusaphid); Melanaphis sacchari (sugarcane aphid); Adelges spp. (adelgids);Phylloxera devastatrix Pergande (pecan phylloxera); Bemisia tabaciGennadius (tobacco whitefly, sweetpotato whitefly); B. argentifoliiBellows & Perring (silverleaf whitefly); Dialeurodes citri Ashmead(citrus whitefly); Trialeurodes abutiloneus (bandedwinged whitefly) andT. vaporariorum Westwood (greenhouse whitefly); Empoasca fabae Harris(potato leafhopper); Laodelphax striatellus Fallen (smaller brownplanthopper); Macrolestes quadrilineatus Forbes (aster leafhopper);Nephotettix cinticeps Uhler (green leafhopper); N. nigropictus St

al (rice leafhopper); Nilaparvata lugens Stal (brown planthopper);Peregrinus maidis Ashmead (corn planthopper); Sogatella furciferaHorvath (white-backed planthopper); Sogatodes orizicola Muir (ricedelphacid); Typhlocyba pomaria McAtee (white apple leafhopper);Erythroneoura spp. (grape leafhoppers); Magicicada septendecimLinnaeus(periodical cicada); Icerya purchasi Maskell (cottony cushion scale);Quadraspidiotus perniciosus Comstock (San Jose scale); Planococcus citriRisso (citrus mealybug); Pseudococcus spp. (other mealybug complex);Cacopsylla pyricola Foerster (pear psylla); Trioza diospyri Ashmead(persimmon psylla).

Agronomically important species of interest from the order Hemipterainclude, but are not limited to: Acrosternum hilare Say (green stinkbug); Anasa tristis De Geer (squash bug); Blissus leucopterusleucopterus Say (chinch bug); Corythuca gossypii Fabricius (cotton lacebug); Cyrtopeltis modesta Distant (tomato bug); Dysdercus suturellusHerrich-Schäffer (cotton stainer); Euschistus servus Say (brown stinkbug); E. variolarius Palisot de Beauvois (one-spotted stink bug);Graptostethus spp. (complex of seed bugs); Leptoglossus corculus Say(leaf-footed pine seed bug); Lygus lineolaris Palisot de Beauvois(tarnished plant bug); L. Hesperus Knight (Western tarnished plant bug);L. pratensis Linnaeus (common meadow bug); L. rugulipennis Poppius(European tarnished plant bug); Lygocoris pabulinus Linnaeus (commongreen capsid); Nezara viridula Linnaeus (southern green stink bug);Oebalus pugnax Fabricius (rice stink bug); Oncopeltus fasciatus Dallas(large milkweed bug); Pseudatomoscelis seriatus Reuter (cottonfleahopper).

Furthermore, embodiments may be effective against Hemiptera such,Calocoris norvegicus Gmelin (strawberry bug); Orthops campestrisLinnaeus; Plesiocoris rugicollis Fallen (apple capsid); Cyrtopeltismodestus Distant (tomato bug); Cyrtopeltis notatus Distant (suckfly);Spanagonicus albofasciatus Reuter (whitemarked fleahopper); Diaphnocorischlorionis Say (honeylocust plant bug); Labopidicola allii Knight (onionplant bug); Pseudatomoscelis seriatus Reuter (cotton fleahopper);Adelphocoris rapidus Say (rapid plant bug); Poecilocapsus lineatusFabricius (four-lined plant bug); Nysius ericae Schilling (false chinchbug); Nysius raphanus Howard (false chinch bug); Nezara viridulaLinnaeus (Southern green stink bug); Eurygaster spp.; Coreidae spp.;Pyrrhocoridae spp.; Tinidae spp.; Blostomatidae spp.; Reduviidae spp.and Cimicidae spp.

Also included are adults and larvae of the order Acari (mites) such asAceria tosichella Keifer (wheat curl mite); Petrobia latens Müller(brown wheat mite); spider mites and red mites in the familyTetranychidae, Panonychus ulmi Koch (European red mite); Tetranychusurticae Koch (two spotted spider mite); (T. mcdanieli McGregor (McDanielmite); T. cinnabarinus Boisduval (carmine spider mite); T. turkestaniUgarov & Nikolski (strawberry spider mite); flat mites in the familyTenuipalpidae, Brevipalpus lewisi McGregor (citrus flat mite); rust andbud mites in the family Eriophyidae and other foliar feeding mites andmites important in human and animal health, i.e., dust mites in thefamily Epidermoptidae, follicle mites in the family Demodicidae, grainmites in the family Glycyphagidae, ticks in the order Ixodidae. Ixodesscapularis Say (deer tick); I. holocyclus Neumann (Australian paralysistick); Dermacentor variabilis Say (American dog tick); Amblyommaamericanum Linnaeus (lone star tick) and scab and itch mites in thefamilies Psoroptidae, Pyemotidae and Sarcoptidae.

Insect pests of the order Thysanura are of interest, such as Lepismasaccharina Linnaeus (silverfish); Thermobia domestica Packard(firebrat).

Additional arthropod pests covered include: spiders in the order Araneaesuch as Loxosceles reclusa Gertsch and Mulaik (brown recluse spider) andthe Latrodectus mactans Fabricius (black widow spider) and centipedes inthe order Scutigeromorpha such as Scutigera coleoptrata Linnaeus (housecentipede).

Insect pest of interest include the superfamily of stink bugs and otherrelated insects including but not limited to species belonging to thefamily Pentatomidae (Nezara viridula, Halyomorpha halys, Piezodorusguildini, Euschistus servus, Acrosternum hilare, Euschistus heros,Euschistus tristigmus, Acrosternum hilare, Dichelops furcatus, Dichelopsmelacanthus, and Bagrada hilaris (Bagrada Bug)), the family Plataspidae(Megacopta cribraria—Bean plataspid) and the family Cydnidae(Scaptocoris castanea—Root stink bug) and Lepidoptera species includingbut not limited to: diamond-back moth, e.g., Helicoverpa zea Boddie;soybean looper, e.g., Pseudoplusia includens Walker and velvet beancaterpillar e.g., Anticarsia gemmatalis Hübner.

Methods for measuring pesticidal activity are well known in the art.See, for example, Czapla and Lang, (1990) J. Econ. Entomol.83:2480-2485; Andrews, et al., (1988) Biochem. J. 252:199-206; Marrone,et al., (1985) J. of Economic Entomology 78:290-293 and U.S. Pat. No.5,743,477, all of which are herein incorporated by reference in theirentirety. Generally, the protein is mixed and used in feeding assays.See, for example Marrone, et al., (1985) J. of Economic Entomology78:290-293. Such assays can include contacting plants with one or morepests and determining the plant's ability to survive and/or cause thedeath of the pests.

Nematodes include parasitic nematodes such as root-knot, cyst and lesionnematodes, including Heterodera spp., Meloidogyne spp. and Globoderaspp.; particularly members of the cyst nematodes, including, but notlimited to, Heterodera glycines (soybean cyst nematode); Heteroderaschachtii (beet cyst nematode); Heterodera avenae (cereal cyst nematode)and Globodera rostochiensis and Globodera pailida (potato cystnematodes). Lesion nematodes include Pratylenchus spp.

Seed Treatment

To protect and to enhance yield production and trait technologies, seedtreatment options can provide additional crop plan flexibility and costeffective control against insects, weeds and diseases. Seed material canbe treated, typically surface treated, with a composition comprisingcombinations of chemical or biological herbicides, herbicide safeners,insecticides, fungicides, germination inhibitors and enhancers,nutrients, plant growth regulators and activators, bactericides,nematocides, avicides and/or molluscicides. These compounds aretypically formulated together with further carriers, surfactants orapplication-promoting adjuvants customarily employed in the art offormulation. The coatings may be applied by impregnating propagationmaterial with a liquid formulation or by coating with a combined wet ordry formulation. Examples of the various types of compounds that may beused as seed treatments are provided in The Pesticide Manual: A WorldCompendium, C. D. S. Tomlin Ed., Published by the British CropProduction Council, which is hereby incorporated by reference.

Some seed treatments that may be used on crop seed include, but are notlimited to, one or more of abscisic acid, acibenzolar-S-methyl,avermectin, amitrol, azaconazole, azospirillum, azadirachtin,azoxystrobin, Bacillus spp. (including one or more of cereus, firmus,megaterium, pumilis, sphaericus, subtilis and/or thuringiensis species),bradyrhizobium spp. (including one or more of betae, canariense,elkanii, iriomotense, japonicum, liaonigense, pachyrhizi and/oryuanmingense), captan, carboxin, chitosan, clothianidin, copper,cyazypyr, difenoconazole, etidiazole, fipronil, fludioxonil,fluoxastrobin, fluquinconazole, flurazole, fluxofenim, harpin protein,imazalil, imidacloprid, ipconazole, isoflavenoids,lipo-chitooligosaccharide, mancozeb, manganese, maneb, mefenoxam,metalaxyl, metconazole, myclobutanil, PCNB, penflufen, penicillium,penthiopyrad, permethrine, picoxystrobin, prothioconazole,pyraclostrobin, rynaxypyr, S-metolachlor, saponin, sedaxane, TCMTB,tebuconazole, thiabendazole, thiamethoxam, thiocarb, thiram,tolclofos-methyl, triadimenol, trichoderma, trifloxystrobin,triticonazole and/or zinc. PCNB seed coat refers to EPA RegistrationNumber 00293500419, containing quintozen and terrazole. TCMTB refers to2-(thiocyanomethylthio) benzothiazole.

Seed varieties and seeds with specific transgenic traits may be testedto determine which seed treatment options and application rates maycomplement such varieties and transgenic traits in order to enhanceyield. For example, a variety with good yield potential but head smutsusceptibility may benefit from the use of a seed treatment thatprovides protection against head smut, a variety with good yieldpotential but cyst nematode susceptibility may benefit from the use of aseed treatment that provides protection against cyst nematode, and soon. Likewise, a variety encompassing a transgenic trait conferringinsect resistance may benefit from the second mode of action conferredby the seed treatment, a variety encompassing a transgenic traitconferring herbicide resistance may benefit from a seed treatment with asafener that enhances the plants resistance to that herbicide, etc.Further, the good root establishment and early emergence that resultsfrom the proper use of a seed treatment may result in more efficientnitrogen use, a better ability to withstand drought and an overallincrease in yield potential of a variety or varieties containing acertain trait when combined with a seed treatment.

Methods for Killing an Insect Pest and Controlling an Insect Population

In some embodiments methods are provided for killing an insect pest,comprising contacting the insect pest with an insecticidally-effectiveamount of a recombinant PIP-72 polypeptide and a polynucleotide encodinga silencing element. In some embodiments methods are provided forkilling an insect pest, comprising contacting the insect pest with aninsecticidally-effective amount one or more recombinant pesticidalprotein(s) of SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8,SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 18, SEQ ID NO:28, SEQ ID NO: 32, any one of SEQ ID NO: 528 -SEQ ID NO: 768, any one ofSEQ ID NO: 825-SEQ ID NO: 844, SEQ ID NO: 771, SEQ ID NO: 772 or SEQ IDNO: 852 or a variant thereof, and one or more silencing elements targetdisclosed in US Patent Application Publication No. US2014/0275208 orUS2015/0257389.

In some embodiments methods are provided for controlling an insect pestpopulation, comprising contacting the insect pest population with aninsecticidally-effective amount of one or more recombinant PIP-72polypeptide(s) and one or more polynucleotides encoding a silencingelement(s). As used herein, “controlling a pest population” or “controlsa pest” refers to any effect on a pest that results in limiting thedamage that the pest causes. Controlling a pest includes, but is notlimited to, killing the pest, inhibiting development of the pest,altering fertility or growth of the pest in such a manner that the pestprovides less damage to the plant, decreasing the number of offspringproduced, producing less fit pests, producing pests more susceptible topredator attack or deterring the pests from eating the plant.

In some embodiments methods are provided for controlling an insect pestpopulation resistant to a pesticidal protein, comprising contacting theinsect pest population with an insecticidally-effective amount of one ormore recombinant PIP-72 polypeptide and a silencing element.

In some embodiments methods are provided for protecting a plant from aninsect pest, comprising expressing in the plant or cell thereof arecombinant polynucleotide encoding one or more PIP-72 polypeptide and asilencing element(s).

Insect Resistance Management (IRM) Strategies

Expression of B. thuringiensis δ-endotoxins in transgenic corn plantshas proven to be an effective means of controlling agriculturallyimportant insect pests (Perlak, et al., 1990; 1993). However, insectshave evolved that are resistant to B. thuringiensis δ-endotoxinsexpressed in transgenic plants. Such resistance, should it becomewidespread, would clearly limit the commercial value of germplasmcontaining genes encoding such B. thuringiensis δ-endotoxins.

One way to increasing the effectiveness of the transgenic insecticidesagainst target pests and contemporaneously reducing the development ofinsecticide-resistant pests is to use provide non-transgenic (i.e.,non-insecticidal protein) refuges (a section of non-insecticidalcrops/corn) for use with transgenic crops producing a singleinsecticidal protein active against target pests. The United StatesEnvironmental Protection Agency(epa.gov/oppbppdl/biopesticides/pips/bt_corn_refuge_2006.htm, which canbe accessed using the www prefix) publishes the requirements for usewith transgenic crops producing a single Bt protein active againsttarget pests. In addition, the National Corn Growers Association, ontheir website:(ncga.com/insect-resistance-management-fact-sheet-bt-corn, which can beaccessed using the www prefix) also provides similar guidance regardingrefuge requirements. Due to losses to insects within the refuge area,larger refuges may reduce overall yield.

Another way of increasing the effectiveness of the transgenicinsecticides against target pests and contemporaneously reducing thedevelopment of insecticide-resistant pests would be to have a repositoryof insecticidal genes that are effective against groups of insect pestsand which manifest their effects through different modes of action.

Expression in a plant of two or more insecticidal compositions toxic tothe same insect species, each insecticide being expressed at efficaciouslevels would be another way to achieve control of the development ofresistance. This is based on the principle that evolution of resistanceagainst two separate modes of action is far more unlikely than only one.Roush, for example, outlines two-toxin strategies, also called“pyramiding” or “stacking,” for management of insecticidal transgeniccrops. (The Royal Society. Phil. Trans. R. Soc. Lond. B. (1998)353:1777-1786). Stacking or pyramiding of two different proteins eacheffective against the target pests and with little or nocross-resistance can allow for use of a smaller refuge. The USEnvironmental Protection Agency requires significantly less (generally5%) structured refuge of non-Bt corn be planted than for single traitproducts (generally 20%). There are various ways of providing the IRMeffects of a refuge, including various geometric planting patterns inthe fields and in-bag seed mixtures, as discussed further by Roush.

In some embodiments the PIP-72 polypeptides and a polynucleotideencoding a silencing element of the disclosure are useful as an insectresistance management strategy in combination (i.e., pyramided) withother pesticidal proteins include but are not limited to Bt toxins,Xenorhabdus sp. or Photorhabdus sp. insecticidal proteins, and the like.

Provided are methods of controlling Lepidoptera and/or Coleoptera insectinfestation(s) in a transgenic plant that promote insect resistancemanagement, comprising expressing in the plant at least two differentinsecticidal proteins having different modes of action.

In some embodiments the methods of controlling Lepidoptera and/orColeoptera insect infestation in a transgenic plant and promoting insectresistance management comprise a PIP-72 polypeptide insecticidal and asilencing element to insects in the order Lepidoptera and/or Coleoptera.

In some embodiments the methods of controlling Lepidoptera and/orColeoptera insect infestation in a transgenic plant and promoting insectresistance management comprise expressing in the transgenic plant aPIP-72 polypeptide and a polynucleotide encoding silencing elementinsecticidal to insects in the order Lepidoptera and/or Coleopterahaving different modes of action.

Also provided are methods of reducing likelihood of emergence ofLepidoptera and/or Coleoptera insect resistance to transgenic plantsexpressing in the plants insecticidal proteins to control the insectspecies, comprising expression of a PIP-72 polypeptide and apolynucleotide encoding a silencing element insecticidal to the insectspecies in combination with a second insecticidal protein to the insectspecies having different modes of action.

Also provided are means for effective Lepidoptera and/or Coleopterainsect resistance management of transgenic plants, comprisingco-expressing at high levels in the plants two or more insecticidalproteins toxic to Lepidoptera and/or Coleoptera insects but eachexhibiting a different mode of effectuating its killing activity,wherein the two or more insecticidal proteins comprise a PIP-72polypeptide and a Cry protein. Also provided are means for effectiveLepidoptera and/or Coleoptera insect resistance management of transgenicplants, comprising co-expressing at high levels in the plants two ormore insecticidal proteins toxic to Lepidoptera and/or Coleopterainsects but each exhibiting a different mode of effectuating its killingactivity, wherein the two or more insecticidal proteins.

The above description of various illustrated embodiments of thedisclosure is not intended to be exhaustive or to limit the invention tothe precise form disclosed. While specific embodiments, and examples,are described herein for illustrative purposes, various equivalentmodifications are possible within the scope, as those skilled in therelevant art will recognize. The teachings provided herein can beapplied to other purposes, other than the examples described above. Theembodiments may be practiced in ways other than those particularlydescribed in the foregoing description and examples. Numerousmodifications and variations of the invention are possible in light ofthe above teachings and, therefore, are within the scope of the appendedclaims.

These and other changes may be made to the embodiments in light of theabove detailed description. In general, in the following claims, theterms used should not be construed to limit the embodiments to thespecific embodiments disclosed in the specification and the claims.

The entire disclosure of each document cited (including patents, patentapplications, journal articles, abstracts, manuals, books or otherdisclosures) in the Background, Detailed Description, and Examples isherein incorporated by reference in their entireties.

Efforts have been made to ensure accuracy with respect to the numbersused (e.g. amounts, temperature, concentrations, etc.) but someexperimental errors and deviations should be allowed for. Unlessotherwise indicated, parts are parts by weight, molecular weight isaverage molecular weight; temperature is in degrees centigrade; andpressure is at or near atmospheric.

EXPERIMENTALS Example 1 Insecticidal Activity of Transgenic PlantsExpressing PIP-72 and dsRNA RyanR Silencing Element

Rootworms assays were performed by infesting plants which had beenrecently transplanted from flats into pots with a volume ofapproximately 3 liters. Soil mix was variable but should be high inpeat, bark chunks and other soil amendments to lighten the medium andpromote aeration and healthy root growth. 2 days after transplanting,plants were infested with 200 western corn rootworm eggs suspended inwater. Eggs were timed so hatch would occur within a few days ofinfestation. Plants were maintained with standard greenhouse practicesof watering and applications of fertilizer. 19 days later, plants wereremoved from pots and the soil washed from the roots to expose thefeeding damage. Ratings were made using the Node Injury Scale developedby Nowatzki et al (2005) J. of Economic Entomology, 98, 1-8. The NodalInjury Score is based on number of root nodes of damage with 0indicating no damage and 3 indicating 3 nodes of roots are eaten to alength of less than 2 centimeters. The stacked constructs showsignificantly reduced feeding damage compared to the negative controls(FIG. 1).

Example 2 Expression of dsRANA RyanR Silencing Element in PIP-72 anddsRNA RyanR Silencing Element Stacked Transgenic Maize

QuantiGene® Plex 2.0 RNA assay (Affymetrix®) was used for detectingdsRNA targeting RyanR (DvSSJ, SEQ ID NO: 993) sense strand of transcriptin transgenic plants. Double strand RNA targeting RyanR was made by Invitro transcription. Purified dsRNA was quantified by OD260 and used asstandard for quantitative detection. Transgenic roots (about 45 mg) werecollected from each individual T0 plant and processed for QuantiGene®detection according to the QuantiGene® 2.0 User Manual. RNA expressiondata were calculated as picogram per mg fresh root (or pg/mg). Thestacked constructs show significant expression of dsRNA targeting RyanR,with no detection in a negative control (FIG. 2).

Example 3 Expression of PIP-72 Polypeptide in PIP-72 and dsRNA RyanRSilencing Element Stacked Transgenic Maize

The absolute expression concentration of PIP-72Aa protein was determinedby using LC-MS/MS (liquid chromatography coupled with tandem massspectrometry) according J Agric Food Chem. 2011 Apr 27; 59(8):3551-8).After being lyophilized and ground, 10 mg of leaf samples were extractedwith 600 μl PBST buffer (phosphate-buffered saline and 0.05% Tween 20).Approximately 500 mg of fresh frozen root samples were extracted with1000 μl PBST buffer. After centrifugation, the supernatant was collectedand total extracted proteins (TEPs) were measured with a Bradford assay.Samples were normalized by TEP. A total of 50 μL of the normalizedextract was added to 100 μL of digestion buffer ABCT (100 mM ammoniumbicarbonate and 0.05% Tween 20). A standard curve was prepared byspiking different amounts of the recombinant protein standard into 50 μLaliquots of negative sample extract. An appropriate amount of thedigestion buffer ABCT was added to each point of the standard curve tokeep total volumes consistent among samples and standards. Samples andstandards were reduced with 6 μL of 0.25 M dithiothreitol at 50° C. for30 min and then alkylated with 6 μL of 0.3 M iodoacetamide at roomtemperature in the dark for 30 min. One μg of trypsin (10 μL) was addedto each sample and digestion was allowed to proceed at 37° C. overnight(˜18 hours) before 10 μL 10% (v/v) formic acid was added. PIP-72Aaprotein was quantified by monitoring its signature tryptic peptideQETWDR with MRM (multiple reaction monitoring) transition of417.7/577.3, using a Waters UPLC (ultra-performance liquidchromatography) coupled with AB SCIEX Q-TRAP 5500. Autosamplertemperature was maintained at 8° C. during analysis. 10 μL volumes wereinjected onto an BEH 50×2.1 mm 1.7 μ C18 column (Waters) maintained at60° C. Mobile phases consisted of 0.1% formic acid (MPA) and 0.1% formicacid in acetonitrile (MPB), and LC was performed at a flow rate of 1.0mL/min with linear gradient of 2-10% MPB in 1.5 min. Proteinconcentrations in the unknown samples were calculated by interpolationinto the standard curve using Analyst version 1.6.2 software (AB Sciex).The stacked constructs show significant expression of PIP-72, with nodetection in a negative control (FIG. 3).

Example 4 Agrobacterium-Mediated StableTransformation of Maize

For Agrobacterium-mediated maize transformation of PIP-72 and dsRNARyanR silencing element stacked transgenic maize, the method of Zhao wasemployed (U.S. Pat. No. 5,981,840 and International Patent PublicationNumber WO 1998/32326). Briefly, immature embryos were isolated frommaize and the embryos contacted with an Agrobacterium Suspension, wherethe bacteria were capable of transferring a polynucleotide encoding aPIP-72 polypeptide and a polynucleotide encoding a silencing elementtargeting RyanR to at least one cell of at least one of the immatureembryos (step 1: the infection step). In this step the immature embryoswere immersed in an Agrobacterium suspension for the initiation ofinoculation. The embryos were co-cultured for a time with theAgrobacterium (step 2: the co-cultivation step). The immature embryoswere cultured on solid medium with antibiotic, but without a selectingagent, for Agrobacterium elimination and for a resting phase for theinfected cells. Next, inoculated embryos were cultured on mediumcontaining a selective agent and growing transformed callus is recovered(step 4: the selection step). The immature embryos were cultured onsolid medium with a selective agent resulting in the selective growth oftransformed cells. The callus was then regenerated into plants (step 5:the regeneration step), and calli grown on selective medium werecultured on solid medium to regenerate the plants.

Transgenic maize plants positive for expression of the insecticidalproteins are tested for pesticidal activity using standard bioassaysknown in the art. Such methods include, for example, root excisionbioassays and whole plant bioassays. See, e.g., US Patent ApplicationPublication Number US 2003/0120054 and International Publication NumberWO 2003/018810.

1. A DNA construct comprising i) a nucleic acid molecule encoding aPIP-72 polypeptide having insecticidal activity and ii) a silencingelement targeting RyanR or RPS10 having insecticidal activity.
 2. TheDNA construct of claim 1, wherein the nucleic acid molecule encoding thePIP-72 polypeptide and silencing element are operably linked to aheterologous regulatory element.
 3. The DNA construct of claim 1,wherein the silencing element is a sense suppression element, anantisense suppression element, a double stranded RNA, a siRNA, a amiRNA,a miRNA, or a hairpin suppression element.
 4. A molecular stackcomprising i) a nucleic acid molecule encoding a PIP-72 polypeptidehaving insecticidal activity and ii) a silencing element targeting RyanRor RPS10 having insecticidal activity.
 5. The molecular stack of claim4, wherein the nucleic acid molecule encoding the PIP-72 polypeptide andsilencing element are operably linked to a heterologous regulatoryelement.
 6. The molecular stack of claim 4, wherein the silencingelement is a sense suppression element, an antisense suppressionelement, a double stranded RNA, a siRNA, a amiRNA, a miRNA, or a hairpinsuppression element.
 7. A breeding stack comprising i) a nucleic acidmolecule encoding a PIP-72 polypeptide having insecticidal activity andii) a Ryanodine receptor or RPS10 silencing element having insecticidalactivity.
 8. The breeding stack of claim 7, wherein the nucleic acidmolecule encoding the PIP-72 polypeptide and the silencing element areeach operably linked to a heterologous regulatory element.
 9. Thebreeding stack of claim 7, wherein the silencing element is a sensesuppression element, an antisense suppression element, a double strandedRNA, a siRNA, a amiRNA, a miRNA, or a hairpin suppression element.
 10. Atransgenic plant or progeny thereof comprising the DNA construct ofclaim
 1. 11. A transgenic plant or progeny thereof comprising themolecular stack of claim
 4. 12. A transgenic plant or progeny thereofcomprising the breeding stack of claim
 7. 13. A composition comprisingi) a nucleic acid molecule encoding a PIP-72 polypeptide havinginsecticidal activity and ii) a silencing element targeting RyanR orRPS10 having insecticidal activity.
 14. The composition of claim 13,wherein the silencing element is a sense suppression element, anantisense suppression element, a double stranded RNA, a siRNA, a amiRNA,a miRNA, or a hairpin suppression element.
 15. A method for controllingan insect pest population comprising contacting the insect pestpopulation with the transgenic plant of claim 10.